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233,605 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Structure Author = "Li, W."

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Search Summary

This query matches 359 Structures.

Refinements

Structure Determination Methodology

experimental (359)

Scientific Name of Source Organism

	Homo sapiens (186)
	Severe acute respiratory syndrome coronavirus 2 (46)
	synthetic construct (33)
	Sus scrofa (31)
	Gallus gallus (26)
	Escherichia coli (23)
	Rattus norvegicus (19)
	Amanita phalloides (16)
	Aequorea victoria (15)
	Bos taurus (10)

More...

Taxonomy

	Eukaryota (268)
	Riboviria (64)
	Bacteria (60)
	other sequences (33)
	Archaea (6)
	Duplodnaviria (2)
	Eukaryota (eukaryotes) (1)

Experimental Method

	X-RAY DIFFRACTION (195)
	ELECTRON MICROSCOPY (161)
	SOLUTION NMR (2)
	SOLID-STATE NMR (1)

Polymer Entity Type

	Protein (356)
	RNA (49)
	DNA (37)

Refinement Resolution (Å)

	1.0 - 1.5 (7)
	1.5 - 2.0 (41)
	2.0 - 2.5 (73)
	2.5 - 3.0 (89)
	3.0 - 3.5 (67)
	3.5 - 4.0 (41)
	4.0 - 4.5 (6)
	> 4.5 (31)

Release Date

	2000 - 2004 (17)
	2005 - 2009 (30)
	2010 - 2014 (43)
	2015 - 2019 (71)
	2020 - 2024 (183)
	2025 - 2029 (15)

Enzyme Classification Name

	Hydrolases (138)
	Transferases (54)
	Oxidoreductases (41)
	Isomerases (20)
	Lyases (15)
	Translocases (8)

Membrane Protein Annotation

	PDBTM (53)
	MemProtMD (29)
	mpstruc (43)
	OPM (33)

Symmetry Type

	Asymmetric (282)
	Cyclic (75)
	Dihedral (7)

SCOP Classification

	Alpha and beta proteins (a+b) (54)
	Alpha and beta proteins (a/b) (34)
	All beta proteins (21)
	All alpha proteins (35)
	Artifacts (26)
	Multi-domain proteins (alpha and beta) (5)
	Small proteins (6)
	Membrane and cell surface proteins and peptides (3)
	Low resolution protein structures (4)

AllSelected

1 to 25 of 359 Structures

Page 1 of 15

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1G7P \| pdb_00001g7p	Download File View File

CRYSTAL STRUCTURE OF MHC CLASS I H-2KB HEAVY CHAIN COMPLEXED WITH BETA-2 MICROGLOBULIN AND YEAST ALPHA-GLUCOSIDASE

Apostolopoulos, V., Yu, M., Corper, A.L., Li, W., McKenzie, I.F., Teyton, L., Wilson, I.A.

(2002) J Mol Biology 318: 1307-1316

Released	2002-07-17
Method	X-RAY DIFFRACTION 1.5 Å
Organisms	Mus musculus Saccharomyces cerevisiae
Macromolecule	ALPHA-GLUCOSIDASE P1 (protein) BETA-2 MICROGLOBULIN (protein) H-2 CLASS I HISTOCOMPATIBILITY ANTIGEN, K-B ALPHA CHAIN (protein)
Unique Ligands	NAG
Unique branched monosaccharides	FUC, NAG

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1H3L \| pdb_00001h3l	Download File View File

N-terminal fragment of SigR from Streptomyces coelicolor

Li, W., Stevenson, C.E.M., Burton, N., Jakimowicz, P., Paget, M.S.B., Buttner, M.J., Lawson, D.M., Kleanthous, C.

(2002) J Mol Biology 323: 225

Released	2002-10-03
Method	X-RAY DIFFRACTION 2.375 Å
Organisms	Streptomyces coelicolor A3(2)
Macromolecule	RNA POLYMERASE SIGMA FACTOR (protein)

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1JT8 \| pdb_00001jt8	Download File View File

ARCHAEAL INITIATION FACTOR-1A, AIF-1A

Hoffman, D.W., Li, W.

(2001) Protein Sci 10: 2426-2438

Released	2001-09-05
Method	SOLUTION NMR
Organisms	Methanocaldococcus jannaschii
Macromolecule	PROBABLE TRANSLATION INITIATION FACTOR 1A (protein)

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1LCS \| pdb_00001lcs	Download File View File

RECEPTOR-BINDING DOMAIN FROM SUBGROUP B FELINE LEUKEMIA VIRUS

Barnett, A.L., Wensel, D.L., Li, W., Fass, D., Cunningham, J.M.

(2003) J Virol 77: 2717-2729

Released	2003-04-08
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Feline leukemia virus strain B/lambda-B1
Macromolecule	FELINE LEUKEMIA VIRUS RECEPTOR-BINDING DOMAIN (protein)
Unique Ligands	TOE
Unique branched monosaccharides	BMA, MAN, NAG, NDG

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1LCY \| pdb_00001lcy	Download File View File

Crystal Structure of the Mitochondrial Serine Protease HtrA2

Li, W., Srinivasula, S.M., Chai, J., Li, P., Wu, J.W., Zhang, Z., Alnemri, E.S., Shi, Y.

(2002) Nat Struct Biol 9: 436-441

Released	2002-05-22
Method	X-RAY DIFFRACTION 2 Å
Organisms	Homo sapiens
Macromolecule	HtrA2 serine protease (protein)

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1MR1 \| pdb_00001mr1	Download File View File

Crystal Structure of a Smad4-Ski Complex

Wu, J.-W., Krawitz, A.R., Chai, J., Li, W., Zhang, F., Luo, K., Shi, Y.

(2002) Cell 111: 357-367

Released	2003-01-21
Method	X-RAY DIFFRACTION 2.85 Å
Organisms	Homo sapiens
Macromolecule	Mothers against decapentaplegic homolog 4 (protein) Ski oncogene (protein)
Unique Ligands	ZN

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1NB8 \| pdb_00001nb8	Download File View File

Structure of the catalytic domain of USP7 (HAUSP)

Hu, M., Li, P., Li, M., Li, W., Yao, T., Wu, J.-W., Gu, W., Cohen, R.E., Shi, Y.

(2002) Cell 111: 1041-1054

Released	2003-01-07
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Homo sapiens
Macromolecule	Ubiquitin carboxyl-terminal hydrolase 7 (protein)

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1NBF \| pdb_00001nbf	Download File View File

Crystal structure of a UBP-family deubiquitinating enzyme in isolation and in complex with ubiquitin aldehyde

Hu, M., Li, P., Li, M., Li, W., Yao, T., Wu, J.-W., Gu, W., Cohen, R.E., Shi, Y.

(2002) Cell 111: 1041-1054

Released	2003-01-07
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Homo sapiens
Macromolecule	Ubiquitin aldehyde (protein) Ubiquitin carboxyl-terminal hydrolase 7 (protein)

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1P6B \| pdb_00001p6b	Download File View File

X-ray structure of phosphotriesterase, triple mutant H254G/H257W/L303T

Hill, C.M., Li, W., Thoden, J.B., Holden, H.M., Raushel, F.M.

(2003) J Am Chem Soc 125: 8990-8991

Released	2003-09-16
Method	X-RAY DIFFRACTION 1.9 Å
Organisms	Flavobacterium sp.
Macromolecule	Parathion hydrolase (protein)
Unique Ligands	EBP, EFS, ZN

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1P6C \| pdb_00001p6c	Download File View File

crystal structure of phosphotriesterase triple mutant H254G/H257W/L303T complexed with diisopropylmethylphosphonate

Hill, C.M., Li, W., Thoden, J.B., Holden, H.M., Raushel, F.M.

(2003) J Am Chem Soc 125: 8990-8991

Released	2003-09-16
Method	X-RAY DIFFRACTION 2 Å
Organisms	Flavobacterium sp.
Macromolecule	Parathion hydrolase (protein)
Unique Ligands	DII, EBP, ZN

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1QZA \| pdb_00001qza	Download File View File

Coordinates of the A/T site tRNA model fitted into the cryo-EM map of EF-Tu ternary complex (GDP.Kirromycin) bound 70S ribosome

Valle, M., Zavialov, A., Li, W., Stagg, S.M., Sengupta, J., Nielsen, R.C., Nissen, P., Harvey, S.C., Ehrenberg, M., Frank, J.

(2003) Nat Struct Biol 10: 899-906

Released	2003-11-04
Method	ELECTRON MICROSCOPY 10 Å
Macromolecule	Phe-tRNA (nucleic acid)

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1QZB \| pdb_00001qzb	Download File View File

Coordinates of the A-site tRNA model fitted into the cryo-EM map of 70S ribosome in the pre-translocational state

Valle, M., Zavialov, A., Li, W., Stagg, S.M., Sengupta, J., Nielsen, R.C., Nissen, P., Harvey, S.C., Ehrenberg, M., Frank, J.

(2003) Nat Struct Biol 10: 899-906

Released	2003-11-04
Method	ELECTRON MICROSCOPY 9 Å
Macromolecule	Phe-tRNA (nucleic acid)

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1QZC \| pdb_00001qzc	Download File View File

Coordinates of S12, SH44, LH69 and SRL separately fitted into the cryo-EM map of EF-Tu ternary complex (GDP.Kirromycin) bound 70S ribosome

Valle, M., Zavialov, A., Li, W., Stagg, S.M., Sengupta, J., Nielsen, R.C., Nissen, P., Harvey, S.C., Ehrenberg, M., Frank, J.

(2003) Nat Struct Biol 10: 899-906

Released	2003-11-04
Method	ELECTRON MICROSCOPY 9 Å
Organisms	Escherichia coli Thermus thermophilus
Macromolecule	30S ribosomal protein S12 (protein) 16S rRNA (nucleic acid) 23S rRNA (nucleic acid)

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1QZD \| pdb_00001qzd	Download File View File

EF-Tu.kirromycin coordinates fitted into the cryo-EM map of EF-Tu ternary complex (GDP.Kirromycin) bound 70S ribosome

Valle, M., Zavialov, A., Li, W., Stagg, S.M., Sengupta, J., Nielsen, R.C., Nissen, P., Harvey, S.C., Ehrenberg, M., Frank, J.

(2003) Nat Struct Biol 10: 899-906

Released	2003-11-04
Method	ELECTRON MICROSCOPY 10 Å
Organisms	Escherichia coli
Macromolecule	Elongation factor Tu (protein)

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1R2W \| pdb_00001r2w	Download File View File

Coordinates of L11 with 58nts of 23S rRNA fitted into the cryo-EM map of the 70S ribosome

Valle, M., Zavialov, A., Li, W., Stagg, S.M., Sengupta, J., Nielsen, R.C., Nissen, P., Harvey, S.C., Ehrenberg, M., Frank, J.

(2003) Nat Struct Biol 10: 899-906

Released	2003-11-04
Method	ELECTRON MICROSCOPY 9 Å
Organisms	Thermotoga maritima
Macromolecule	50S ribosomal protein L11 (protein) 58nts of 23S rRNA (nucleic acid)

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1R2X \| pdb_00001r2x	Download File View File

Coordinates of L11 with 58nts of 23S rRNA fitted into the cryo-EM map of EF-Tu ternary complex (GDP.Kirromycin) bound 70S ribosome

Valle, M., Zavialov, A., Li, W., Stagg, S.M., Sengupta, J., Nielsen, R.C., Nissen, P., Harvey, S.C., Ehrenberg, M., Frank, J.

(2003) Nat Struct Biol 10: 899-906

Released	2003-11-04
Method	ELECTRON MICROSCOPY 9 Å
Organisms	Thermotoga maritima
Macromolecule	50S ribosomal protein L11 (protein) 58nts of 23S rRNA (nucleic acid)

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1TB6 \| pdb_00001tb6	Download File View File

2.5A Crystal Structure of the Antithrombin-Thrombin-Heparin Ternary Complex

Li, W., Johnson, D.J., Esmon, C.T., Huntington, J.A.

(2004) Nat Struct Mol Biol 11: 857-862

Released	2004-08-17
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Homo sapiens
Macromolecule	Antithrombin-III (protein) thrombin (protein)
Unique Ligands	MPD, NAG
Unique branched monosaccharides	BMA, FUC, GU0, GU1, GU2, GU3, GU4, GU5, GU6, GU8, GU9, MAN, NAG

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1Z6T \| pdb_00001z6t	Download File View File

Structure of the apoptotic protease-activating factor 1 bound to ADP

Riedl, S.J., Li, W., Chao, Y., Schwarzenbacher, R., Shi, Y.

(2005) Nature 434: 926-933

Released	2005-04-19
Method	X-RAY DIFFRACTION 2.21 Å
Organisms	Homo sapiens
Macromolecule	Apoptotic protease activating factor 1 (protein)
Unique Ligands	ADP

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1ZN0 \| pdb_00001zn0	Download File View File

Coordinates of RRF and EF-G fitted into Cryo-EM map of the 50S subunit bound with both EF-G (GDPNP) and RRF

Gao, N., Zavialov, A.V., Li, W., Sengupta, J., Valle, M., Gursky, R.P., Ehrenberg, M., Frank, J.

(2005) Mol Cell 18: 663-674

Released	2005-06-14
Method	ELECTRON MICROSCOPY 15.5 Å
Organisms	Escherichia coli
Macromolecule	ELONGATION FACTOR G (protein) Ribosome recycling factor (protein) 16S RIBOSOMAL RNA (nucleic acid)

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1ZN1 \| pdb_00001zn1	Download File View File

Coordinates of RRF fitted into Cryo-EM map of the 70S post-termination complex

Gao, N., Zavialov, A.V., Li, W., Sengupta, J., Valle, M., Gursky, R.P., Ehrenberg, M., Frank, J.

(2005) Mol Cell 18: 663-674

Released	2005-06-14
Method	ELECTRON MICROSCOPY 14.1 Å
Organisms	Escherichia coli
Macromolecule	30S ribosomal protein S12 (protein) Ribosome recycling factor (protein) ribosomal 16S RNA (nucleic acid) ribosomal 23S RNA (nucleic acid)

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1ZR2 \| pdb_00001zr2	Download File View File

Structure of a Synaptic gamma-delta Resolvase Tetramer Covalently Linked to two Cleaved DNAs

Li, W., Kamtekar, S., Xiong, Y., Sarkis, G.J., Grindley, N.D., Steitz, T.A.

(2005) Science 309: 1210-1215

Released	2005-08-30
Method	X-RAY DIFFRACTION 3.9 Å
Organisms	Escherichia coli
Macromolecule	Transposon gamma-delta resolvase (protein) AAA (nucleic acid) TCAGTGTCCGATAATTTAT (nucleic acid) TTATCGGACACTG (nucleic acid)

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1ZR4 \| pdb_00001zr4	Download File View File

Structure of a Synaptic gamma-delta Resolvase Tetramer Covalently linked to two Cleaved DNAs

Li, W., Kamtekar, S., Xiong, Y., Sarkis, G.J., Grindley, N.D., Steitz, T.A.

(2005) Science 309: 1210-1215

Released	2005-08-30
Method	X-RAY DIFFRACTION 3.4 Å
Organisms	Escherichia coli
Macromolecule	Transposon gamma-delta resolvase (protein) AAA (nucleic acid) TCAGTGTCCGATAATTTAT (nucleic acid) TTATCGGACACTG (nucleic acid)

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2AJF \| pdb_00002ajf	Download File View File

Structure of SARS coronavirus spike receptor-binding domain complexed with its receptor

Li, F., Li, W., Farzan, M., Harrison, S.C.

(2005) Science 309: 1864-1868

Released	2005-09-20
Method	X-RAY DIFFRACTION 2.9 Å
Organisms	Homo sapiens Severe acute respiratory syndrome-related coronavirus
Macromolecule	Angiotensin-converting enzyme-Related Carboxypeptidase (Ace2) (protein) SARS-coronavirus spike protein (protein)
Unique Ligands	CL, NAG, ZN
Unique branched monosaccharides	BMA, NAG

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2B5T \| pdb_00002b5t	Download File View File

2.1 Angstrom structure of a nonproductive complex between antithrombin, synthetic heparin mimetic SR123781 and two S195A thrombin molecules

Johnson, D.J., Li, W., Luis, S.A., Carrell, R.W., Huntington, J.A.

(2006) J Biological Chem 281: 35478-35486

Released	2006-09-19
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Homo sapiens
Macromolecule	Antithrombin-III (protein) Thrombin (protein)
Unique Ligands	GOL, NAG, SO4
Unique branched monosaccharides	BMA, FUC, GU0, GU1, GU2, GU3, GU4, GU5, GU6, GU8, GU9, MAN, NAG

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2C6C \| pdb_00002c6c	Download File View File

membrane-bound glutamate carboxypeptidase II (GCPII) in complex with GPI-18431 (S)-2-(4-iodobenzylphosphonomethyl)-pentanedioic acid

Mesters, J.R., Barinka, C., Li, W., Tsukamoto, T., Majer, P., Slusher, B.S., Konvalinka, J., Hilgenfeld, R.

(2006) EMBO J 25: 1375

Released	2006-02-15
Method	X-RAY DIFFRACTION 2 Å
Organisms	Homo sapiens
Macromolecule	GLUTAMATE CARBOXYPEPTIDASE II (protein)
Unique Ligands	24I, CA, CL, NAG, ZN
Unique branched monosaccharides	MAN, NAG

1 to 25 of 359 Structures

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Structure Determination Methodology

Scientific Name of Source Organism

Taxonomy

Experimental Method

Polymer Entity Type

Refinement Resolution (Å)

Release Date

Enzyme Classification Name

Membrane Protein Annotation

Symmetry Type

SCOP Classification

1G7P | pdb_00001g7p

1H3L | pdb_00001h3l

1JT8 | pdb_00001jt8

1LCS | pdb_00001lcs

1LCY | pdb_00001lcy

1MR1 | pdb_00001mr1

1NB8 | pdb_00001nb8

1NBF | pdb_00001nbf

1P6B | pdb_00001p6b

1P6C | pdb_00001p6c

1QZA | pdb_00001qza

1QZB | pdb_00001qzb

1QZC | pdb_00001qzc

1QZD | pdb_00001qzd

1R2W | pdb_00001r2w

1R2X | pdb_00001r2x

1TB6 | pdb_00001tb6

1Z6T | pdb_00001z6t

1ZN0 | pdb_00001zn0

1ZN1 | pdb_00001zn1

1ZR2 | pdb_00001zr2

1ZR4 | pdb_00001zr4

2AJF | pdb_00002ajf

2B5T | pdb_00002b5t

2C6C | pdb_00002c6c