RCSB PDB: Search

Warning You are using a web browser that we do not support. Our website will not work properly. Please update to a newer version or download a new web browser, such as Chrome or Firefox.

Help

Help

RCSB PDB

Deposit
- PDBx/mmCIF file
- pdb_extract
- SF-Tool
- Ligand Expo
- MAXIT
- Validation Server
- Validation API
- Information for Journals
- Validation Task Forces
- wwPDB OneDep System
- PDB-IHM
Search
Visualize
Analyze
Download
Learn
- Training Courses
- Guide to PDB Data
- Molecule of the Month
- Educational Resources
- Curricula
- Browse
- News
- SciArt Galleries
- Irving Geis
- David Goodsell
About
Careers
COVID-19

233,605 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

	Include CSM
Advanced Search \| Browse Annotations		Help

Search
Query History
Browse Annotations
MyPDB

QUERY: Citation Author = "Xu, Y."

MyPDB Login

Search API

Advanced Search Query Builder

Help

Full Text

Structure Attributes

Help

NOT

Count

Add Subquery

Chemical Attributes

Sequence Similarity

Sequence Motif

Structure Similarity

Structure Motif

Chemical Similarity

Return

grouped by

Include Computed Structure Models (CSM)

Count

Clear

Search Summary

This query matches 1,360 Structures.

Refinements

Structure Determination Methodology

experimental (1,360)

Scientific Name of Source Organism

	Homo sapiens (708)
	Mus musculus (97)
	synthetic construct (97)
	Severe acute respiratory syndrome coronavirus 2 (62)
	Escherichia coli (55)
	Sus scrofa (37)
	Arabidopsis thaliana (27)
	Pseudomonas aeruginosa PAO1 (21)
	Rattus norvegicus (21)
	Bos taurus (17)

More...

Taxonomy

	Eukaryota (952)
	Bacteria (350)
	Riboviria (152)
	other sequences (97)
	Varidnaviria (14)
	Duplodnaviria (12)
	Eukaryota (eukaryotes) (8)
	Archaea (7)
	unclassified sequences (6)
	Monodnaviria (4)

More...

Experimental Method

	X-RAY DIFFRACTION (936)
	ELECTRON MICROSCOPY (364)
	SOLUTION NMR (60)

Polymer Entity Type

	Protein (1,346)
	DNA (87)
	RNA (52)

Refinement Resolution (Å)

	0.5 - 1.0 (1)
	1.0 - 1.5 (65)
	1.5 - 2.0 (255)
	2.0 - 2.5 (306)
	2.5 - 3.0 (310)
	3.0 - 3.5 (226)
	3.5 - 4.0 (66)
	4.0 - 4.5 (29)
	> 4.5 (42)

Release Date

	1995 - 1999 (13)
	2000 - 2004 (44)
	2005 - 2009 (91)
	2010 - 2014 (205)
	2015 - 2019 (330)
	2020 - 2024 (634)
	2025 - 2029 (43)

Enzyme Classification Name

	Hydrolases (419)
	Transferases (287)
	Oxidoreductases (82)
	Lyases (34)
	Isomerases (34)
	Ligases (31)
	Translocases (4)

Membrane Protein Annotation

	PDBTM (165)
	MemProtMD (105)
	mpstruc (105)
	OPM (92)

Symmetry Type

	Asymmetric (868)
	Cyclic (413)
	Dihedral (88)
	Helical (7)
	Icosahedral (2)
	Octahedral (1)
	Tetrahedral (1)

SCOP Classification

	Alpha and beta proteins (a/b) (100)
	All alpha proteins (110)
	Alpha and beta proteins (a+b) (107)
	All beta proteins (86)
	Artifacts (60)
	Coiled coil proteins (30)
	Small proteins (29)
	Membrane and cell surface proteins and peptides (4)
	Multi-domain proteins (alpha and beta) (5)
	Low resolution protein structures (2)

More...

AllSelected

1 to 25 of 1,360 Structures

Page 1 of 55

Sort by

Explore in 3D

1B99 \| pdb_00001b99	Download File View File

3'-FLUORO-URIDINE DIPHOSPHATE BINDING TO NUCLEOSIDE DIPHOSPHATE KINASE

Janin, J., Xu, Y.

(1999) Biochemistry 38: 7265-7272

Released	1999-06-28
Method	X-RAY DIFFRACTION 2.7 Å
Organisms	Dictyostelium discoideum
Macromolecule	PROTEIN (NUCLEOSIDE DIPHOSPHATE KINASE) (protein)
Unique Ligands	FUP, POP

Explore in 3D

1BIK \| pdb_00001bik	Download File View File

X-RAY STRUCTURE OF BIKUNIN FROM THE HUMAN INTER-ALPHA-INHIBITOR COMPLEX

Xu, Y., Carr, P.D., Guss, J.M., Ollis, D.L.

(1998) J Mol Biology 276: 955-966

Released	1999-03-16
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Homo sapiens
Macromolecule	BIKUNIN (protein)
Unique Ligands	NAG, SO4

Explore in 3D

1BZY \| pdb_00001bzy	Download File View File

HUMAN HGPRTASE WITH TRANSITION STATE INHIBITOR

Shi, W., Li, C., Tyler, P.C., Furneaux, R.H., Grubmeyer, C., Schramm, V.L., Almo, S.C.

(1999) Nat Struct Biol 6: 588-593

Released	1999-06-22
Method	X-RAY DIFFRACTION 2 Å
Organisms	Homo sapiens
Macromolecule	HYPOXANTHINE-GUANINE PHOSPHORIBOSYLTRANSFERASE (protein)
Unique Ligands	IMU, MG, POP

Explore in 3D

1CXR \| pdb_00001cxr	Download File View File

AUTOMATED 2D NOESY ASSIGNMENT AND STRUCTURE CALCULATION OF CRAMBIN(S22/I25) WITH SELF-CORRECTING DISTANCE GEOMETRY BASED NOAH/DIAMOD PROGRAMS

Xu, Y., Wu, J., Gorenstein, D., Braun, W.

(1999) J Magn Reson (1969 136: 76-85

Released	1999-09-07
Method	SOLUTION NMR
Organisms	Crambe hispanica subsp. abyssinica
Macromolecule	CRAMBIN (protein)

Explore in 3D

1D6N \| pdb_00001d6n	Download File View File

TERNARY COMPLEX STRUCTURE OF HUMAN HGPRTASE, PRPP, MG2+, AND THE INHIBITOR HPP REVEALS THE INVOLVEMENT OF THE FLEXIBLE LOOP IN SUBSTRATE BINDING

Balendiran, G.K.

(1999) Protein Sci 8: 1023-1031

Released	1999-12-30
Method	X-RAY DIFFRACTION 2.7 Å
Organisms	Homo sapiens
Macromolecule	PROTEIN (HYPOXANTHINE-GUANINE PHOSPHORIBOSYLTRANSFERASE) (protein)
Unique Ligands	MG, PPO, PRP

Explore in 3D

1DLE \| pdb_00001dle	Download File View File

FACTOR B SERINE PROTEASE DOMAIN

Jing, H., Xu, Y., Carson, M., Moore, D., Macon, K.J., Volanakis, J.E., Narayana, S.V.

(2000) EMBO J 19: 164-173

Released	2000-12-13
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Homo sapiens
Macromolecule	COMPLEMENT FACTOR B (protein)

Explore in 3D

1DU9 \| pdb_00001du9	Download File View File

SOLUTION STRUCTURE OF BMP02, A NATURAL SCORPION TOXIN WHICH BLOCKS APAMIN-SENSITIVE CALCIUM-ACTIVATED POTASSIUM CHANNELS, 25 STRUCTURES

Xu, Y., Wu, J., Pei, J., Shi, Y., Ji, Y., Tong, Q.

(2000) Biochemistry 39: 13669-13675

Released	2000-02-04
Method	SOLUTION NMR
Organisms	Olivierus martensii
Macromolecule	BMP02 NEUROTOXIN (protein)

Explore in 3D

1EP5 \| pdb_00001ep5	Download File View File

CRYSTAL STRUCTURE OF THE CONSERVED CORE DOMAIN OF VENEZUALAN EQUINE ENCEPHALITIS CAPSID PROTEIN

Watowich, S.J.

To be published

Released	2003-07-08
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Venezuelan equine encephalitis virus
Macromolecule	CAPSID PROTEIN C (protein)
Unique Ligands	SO4, URE

Explore in 3D

1EP6 \| pdb_00001ep6	Download File View File

CRYSTAL STRUCTURE OF THE CONSERVED CORE DOMAIN OF VENEZUALAN EQUINE ENCEPHALITIS CAPSID PROTEIN

Watowich, S.J.

To be published

Released	2003-07-08
Method	X-RAY DIFFRACTION 2.45 Å
Organisms	Venezuelan equine encephalitis virus
Macromolecule	CAPSID PROTEIN C (protein)

Explore in 3D

1FYV \| pdb_00001fyv	Download File View File

CRYSTAL STRUCTURE OF THE TIR DOMAIN OF HUMAN TLR1

Xu, Y., Tao, X., Shen, B., Horng, T., Medzhitov, R., Manley, J.L., Tong, L.

(2000) Nature 408: 111-115

Released	2000-11-22
Method	X-RAY DIFFRACTION 2.9 Å
Organisms	Homo sapiens
Macromolecule	TOLL-LIKE RECEPTOR 1 (protein)

Explore in 3D

1FYW \| pdb_00001fyw	Download File View File

CRYSTAL STRUCTURE OF THE TIR DOMAIN OF HUMAN TLR2

Xu, Y., Tao, X., Shen, B., Horng, T., Medzhitov, R., Manley, J.L., Tong, L., Northeast Structural Genomics Consortium (NESG)

(2000) Nature 408: 111-115

Released	2000-11-22
Method	X-RAY DIFFRACTION 3 Å
Organisms	Homo sapiens
Macromolecule	TOLL-LIKE RECEPTOR 2 (protein)

Explore in 3D

1FYX \| pdb_00001fyx	Download File View File

CRYSTAL STRUCTURE OF P681H MUTANT OF TIR DOMAIN OF HUMAN TLR2

Xu, Y., Tao, X., Shen, B., Horng, T., Medzhitov, R., Manley, J.L., Tong, L.

(2000) Nature 408: 111-115

Released	2000-11-22
Method	X-RAY DIFFRACTION 2.8 Å
Organisms	Homo sapiens
Macromolecule	TOLL-LIKE RECEPTOR 2 (protein)

Explore in 3D

1GNK \| pdb_00001gnk	Download File View File

GLNK, A SIGNAL PROTEIN FROM E. COLI

Xu, Y., Cheah, E., Carr, P.D., Vanheeswijk, W.C., Westerhoff, H.V., Vasudevan, S.G., Ollis, D.L.

(1998) J Mol Biology 282: 149-165

Released	1999-07-23
Method	X-RAY DIFFRACTION 2 Å
Organisms	Escherichia coli
Macromolecule	PROTEIN (GLNK) (protein)
Unique Ligands	SO4

Explore in 3D

1HIY \| pdb_00001hiy	Download File View File

Binding of nucleotides to NDP kinase

Cervoni, L., Lascu, I., Xu, Y., Gonin, P., Morr, M., Merouani, M., Janin, J., Giartoso, A.

(2001) Biochemistry 40: 4583

Released	2001-05-31
Method	X-RAY DIFFRACTION 2.6 Å
Organisms	Dictyostelium discoideum
Macromolecule	NUCLEOSIDE DIPHOSPHATE KINASE (protein)
Unique Ligands	3AN

Explore in 3D

1HMP \| pdb_00001hmp	Download File View File

THE CRYSTAL STRUCTURE OF HUMAN HYPOXANTHINE-GUANINE PHOSPHORIBOSYLTRANSFERASE WITH BOUND GMP

Eads, J.C., Scapin, G., Xu, Y., Grubmeyer, C., Sacchettini, J.C.

(1994) Cell 78: 325-334

Released	1995-06-03
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Homo sapiens
Macromolecule	HYPOXANTHINE GUANINE PHOSPHORIBOSYL-TRANSFERASE (protein)
Unique Ligands	5GP

Explore in 3D

1HUV \| pdb_00001huv	Download File View File

CRYSTAL STRUCTURE OF A SOLUBLE MUTANT OF THE MEMBRANE-ASSOCIATED (S)-MANDELATE DEHYDROGENASE FROM PSEUDOMONAS PUTIDA AT 2.15A RESOLUTION

Mathews, F.S., Sukumar, N.

(2001) Biochemistry 40: 9870-9878

Released	2001-09-19
Method	X-RAY DIFFRACTION 2.15 Å
Organisms	Pseudomonas putida Spinacia oleracea
Macromolecule	L(+)-MANDELATE DEHYDROGENASE (protein)
Unique Ligands	FMN, MES, SO4

Explore in 3D

1HW1 \| pdb_00001hw1	Download File View File

THE FADR-DNA COMPLEX: TRANSCRIPTIONAL CONTROL OF FATTY ACID METABOLISM IN ESCHERICHIA COLI

Xu, Y., Heath, R.J., Li, Z., Rock, C.O., White, S.W.

(2001) J Biological Chem 276: 17373-17379

Released	2001-01-24
Method	X-RAY DIFFRACTION 1.5 Å
Organisms	Escherichia coli
Macromolecule	FATTY ACID METABOLISM REGULATOR PROTEIN (protein)
Unique Ligands	SO4, ZN

Explore in 3D

1HW2 \| pdb_00001hw2	Download File View File

FADR-DNA COMPLEX: TRANSCRIPTIONAL CONTROL OF FATTY ACID METABOLISM IN ECHERICHIA COLI

Xu, Y., Heath, R.J., Li, Z., Rock, C.O., White, S.W.

(2001) J Biological Chem 276: 17373-17379

Released	2001-01-22
Method	X-RAY DIFFRACTION 3.25 Å
Organisms	Escherichia coli
Macromolecule	FATTY ACID METABOLISM REGULATOR PROTEIN (protein) 5'-D(CPGPAPTPCPTPGPGPTPCPCPGPAPCPCPAPGPAPTPGPCPT)-3' (nucleic acid) 5'-D(GCPAPTPCPTPGPGPTPCPGPGPAPCPCPAPGPAPTPCPGPA)-3' (nucleic acid)
Unique Ligands	MG

Explore in 3D

1J2T \| pdb_00001j2t	Download File View File

Creatininase Mn

Yoshimoto, T., Tanaka, N., Kanada, N., Inoue, T., Nakajima, Y., Haratake, M., Nakamura, K.T., Xu, Y., Ito, K.

(2004) J Mol Biology 337: 399-416

Released	2004-01-27
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Pseudomonas putida
Macromolecule	creatinine amidohydrolase (protein)
Unique Ligands	MN, SO4, ZN

Explore in 3D

1J2U \| pdb_00001j2u	Download File View File

Creatininase Zn

Yoshimoto, T., Tanaka, N., Kanada, N., Inoue, T., Nakajima, Y., Haratake, M., Nakamura, K.T., Xu, Y., Ito, K.

(2004) J Mol Biology 337: 399-416

Released	2004-01-27
Method	X-RAY DIFFRACTION 1.85 Å
Organisms	Pseudomonas putida
Macromolecule	creatinine amidohydrolase (protein)
Unique Ligands	SO4, ZN

Explore in 3D

1K44 \| pdb_00001k44	Download File View File

Mycobacterium tuberculosis Nucleoside Diphosphate Kinase

Chen, Y., Morera, S., Lascu, I., Janin, J.

(2002) Proteins 47: 556-557

Released	2002-05-15
Method	X-RAY DIFFRACTION 2.6 Å
Organisms	Mycobacterium tuberculosis
Macromolecule	Nucleoside Diphosphate Kinase (protein)

Explore in 3D

1K99 \| pdb_00001k99	Download File View File

Solution Structure of the first HMG box in human Upstream binding factor

Xu, Y., Yang, W., Wu, J., Shi, Y.

(2002) Biochemistry 41: 5415-5420

Released	2001-11-14
Method	SOLUTION NMR
Organisms	Homo sapiens
Macromolecule	Upstream binding factor 1 (protein)

Explore in 3D

1KKX \| pdb_00001kkx	Download File View File

Solution structure of the DNA-binding domain of ADR6

Tu, X., Wu, J., Xu, Y., Shi, Y.

(2001) J Biomol NMR 21: 187-188

Released	2002-07-17
Method	SOLUTION NMR
Organisms	Saccharomyces cerevisiae
Macromolecule	Transcription regulatory protein ADR6 (protein)

Explore in 3D

1KN5 \| pdb_00001kn5	Download File View File

SOLUTION STRUCTURE OF ARID DOMAIN OF ADR6 FROM SACCHAROMYCES CEREVISIAE

Tu, X., Wu, J., Xu, Y., Shi, Y.

(2001) J Biomol NMR 21: 187-188

Released	2002-07-17
Method	SOLUTION NMR
Organisms	Saccharomyces cerevisiae
Macromolecule	Transcription regulatory protein ADR6 (protein)

Explore in 3D

1KSB \| pdb_00001ksb	Download File View File

Relationship of Solution and Protein-Bound Structures of DNA Duplexes with the Major Intrastrand Cross-Link Lesions Formed on Cisplatin Binding to DNA

Marzilli, L.G., Saad, J.S., Kuklenyik, Z., Keating, K.A., Xu, Y.

(2001) J Am Chem Soc 123: 2764-2770

Released	2002-01-17
Method	SOLUTION NMR
Macromolecule	5'-D(APGPGPCPCPGPGPAPG)-3' (nucleic acid) 5'-D(CPTPCPCPGPGPCPCPT)-3' (nucleic acid)
Unique Ligands	CPT

1 to 25 of 1,360 Structures

Page 1 of 55

Sort by

About
About Us
Citing Us
Publications
Team
Careers
Usage & Privacy

Support
Contact Us
Help
Website FAQ
Glossary
Service Status

RCSB PDB is hosted by

RCSB PDB is a member of the

RCSB Partners
Nucleic Acid Knowledgebase

wwPDB Partners
RCSB PDB
PDBe
PDBj
BMRB
EMDB

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.

Prepare Data

Validate Data

Deposit Data

Help and Resources

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

1B99 | pdb_00001b99

1BIK | pdb_00001bik

1BZY | pdb_00001bzy

1CXR | pdb_00001cxr

1D6N | pdb_00001d6n

1DLE | pdb_00001dle

1DU9 | pdb_00001du9

1EP5 | pdb_00001ep5

1EP6 | pdb_00001ep6

1FYV | pdb_00001fyv

1FYW | pdb_00001fyw

1FYX | pdb_00001fyx

1GNK | pdb_00001gnk

1HIY | pdb_00001hiy

1HMP | pdb_00001hmp

1HUV | pdb_00001huv

1HW1 | pdb_00001hw1

1HW2 | pdb_00001hw2

1J2T | pdb_00001j2t

1J2U | pdb_00001j2u

1K44 | pdb_00001k44

1K99 | pdb_00001k99

1KKX | pdb_00001kkx

1KN5 | pdb_00001kn5

1KSB | pdb_00001ksb