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234,136 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Structure Author = "Stoddard, B.L."

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Search Summary

This query matches 193 Structures.

Refinements

Structure Determination Methodology

experimental (193)

Scientific Name of Source Organism

	synthetic construct (83)
	Escherichia coli (21)
	Chlamydomonas reinhardtii (11)
	Saccharomyces cerevisiae (10)
	Homo sapiens (8)
	Physarum polycephalum (7)
	Brevibacillus brevis (4)
	Tequatrovirus T4 (4)
	Acinetobacter sp. NEB 394 (3)
	Bos taurus (3)

More...

Taxonomy

	other sequences (83)
	Eukaryota (58)
	Bacteria (56)
	Duplodnaviria (6)
	unclassified sequences (3)
	Archaea (2)

Experimental Method

	X-RAY DIFFRACTION (184)
	ELECTRON MICROSCOPY (9)

Polymer Entity Type

	Protein (190)
	DNA (71)
	RNA (5)

Refinement Resolution (Å)

	1.0 - 1.5 (7)
	1.5 - 2.0 (29)
	2.0 - 2.5 (75)
	2.5 - 3.0 (49)
	3.0 - 3.5 (26)
	3.5 - 4.0 (4)
	4.0 - 4.5 (1)
	> 4.5 (2)

Release Date

	1990 - 1994 (5)
	1995 - 1999 (20)
	2000 - 2004 (35)
	2005 - 2009 (20)
	2010 - 2014 (20)
	2015 - 2019 (53)
	2020 - 2024 (39)
	2025 - 2029 (1)

Enzyme Classification Name

	Hydrolases (58)
	Transferases (12)
	Oxidoreductases (11)
	Isomerases (2)
	Ligases (1)
	Lyases (1)

Membrane Protein Annotation

OPM (2)

Symmetry Type

	Asymmetric (92)
	Cyclic (87)
	Dihedral (21)

SCOP Classification

	Alpha and beta proteins (a+b) (29)
	Alpha and beta proteins (a/b) (33)
	All beta proteins (16)
	Artifacts (10)
	All alpha proteins (4)
	Designed proteins (1)

AllSelected

1 to 25 of 193 Structures

Page 1 of 8

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1A3W \| pdb_00001a3w	Download File View File

PYRUVATE KINASE FROM SACCHAROMYCES CEREVISIAE COMPLEXED WITH FBP, PG, MN2+ AND K+

Jurica, M.S., Mesecar, A., Heath, P.J., Shi, W., Nowak, T., Stoddard, B.L.

(1998) Structure 6: 195-210

Released	1998-05-27
Method	X-RAY DIFFRACTION 3 Å
Organisms	Saccharomyces cerevisiae
Macromolecule	PYRUVATE KINASE (protein)
Unique Ligands	FBP, K, MN, PGA

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1A3X \| pdb_00001a3x	Download File View File

PYRUVATE KINASE FROM SACCHAROMYCES CEREVISIAE COMPLEXED WITH PG, MN2+ AND K+

Jurica, M.S., Mesecar, A., Heath, P.J., Shi, W., Nowak, T., Stoddard, B.L.

(1998) Structure 6: 195-210

Released	1998-05-27
Method	X-RAY DIFFRACTION 3 Å
Organisms	Saccharomyces cerevisiae
Macromolecule	PYRUVATE KINASE (protein)
Unique Ligands	K, MN, PGA

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1A73 \| pdb_00001a73	Download File View File

INTRON-ENCODED ENDONUCLEASE I-PPOI COMPLEXED WITH DNA

Flick, K.E., Monnat Junior, R.J., Stoddard, B.L.

(1998) Nature 394: 96-101

Released	1998-10-14
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Physarum polycephalum
Macromolecule	INTRON 3 (I-PPO) ENCODED ENDONUCLEASE (protein) DNA (5'-D(TPTPGPAPCPTPCPTPCPTPTPAPA)-3') (nucleic acid) DNA (5'-D(PGPAPGPAPGPTPCP*A)-3') (nucleic acid)
Unique Ligands	MG, ZN

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1AF5 \| pdb_00001af5	Download File View File

GROUP I MOBILE INTRON ENDONUCLEASE

Heath, P.J., Stephens, K.M., Monnat Junior, R.J., Stoddard, B.L.

(1997) Nat Struct Biol 4: 468-476

Released	1997-07-23
Method	X-RAY DIFFRACTION 3 Å
Organisms	Chlamydomonas reinhardtii
Macromolecule	I-CREI (protein)

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1AI2 \| pdb_00001ai2	Download File View File

ISOCITRATE DEHYDROGENASE COMPLEXED WITH ISOCITRATE, NADP+, AND CALCIUM (FLASH-COOLED)

Stoddard, B.L., Mesecar, A., Koshland Junior, D.E.

(1997) Science 277: 202-206

Released	1997-10-15
Method	X-RAY DIFFRACTION 1.9 Å
Organisms	Escherichia coli
Macromolecule	ISOCITRATE DEHYDROGENASE (protein)
Unique Ligands	ICA, NAP

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1AI3 \| pdb_00001ai3	Download File View File

ORBITAL STEERING IN THE CATALYTIC POWER OF ENZYMES: SMALL STRUCTURAL CHANGES WITH LARGE CATALYTIC CONSEQUENCES

Stoddard, B.L., Mesecar, A., Koshland Junior, D.E.

(1997) Science 277: 202-206

Released	1997-11-12
Method	X-RAY DIFFRACTION 1.9 Å
Organisms	Escherichia coli
Macromolecule	ISOCITRATE DEHYDROGENASE (protein)
Unique Ligands	ICT, MG, NDO

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1B0A \| pdb_00001b0a	Download File View File

5,10, METHYLENE-TETRAHYDROPHOLATE DEHYDROGENASE/CYCLOHYDROLASE FROM E COLI.

Shen, B.W., Dyer, D., Huang, J.-Y., D'Ari, L., Rabinowitz, J., Stoddard, B.L.

(1999) Protein Sci 8: 1342-1349

Released	1999-06-29
Method	X-RAY DIFFRACTION 2.56 Å
Organisms	Escherichia coli K-12
Macromolecule	PROTEIN (FOLD BIFUNCTIONAL PROTEIN) (protein)

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1BL5 \| pdb_00001bl5	Download File View File

ISOCITRATE DEHYDROGENASE FROM E. COLI SINGLE TURNOVER LAUE STRUCTURE OF RATE-LIMITED PRODUCT COMPLEX, 10 MSEC TIME RESOLUTION

Stoddard, B.L., Cohen, B., Brubaker, M., Mesecar, A., Koshland Junior, D.E.

(1998) Nat Struct Biol 5: 891-897

Released	1999-05-04
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Escherichia coli
Macromolecule	ISOCITRATE DEHYDROGENASE (protein)
Unique Ligands	AKG, MG, NAP

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1BP7 \| pdb_00001bp7	Download File View File

GROUP I MOBILE INTRON ENDONUCLEASE I-CREI COMPLEXED WITH HOMING SITE DNA

Jurica, M.S., Monnat Junior, R.J., Stoddard, B.L.

(1998) Mol Cell 2: 469-476

Released	1999-01-06
Method	X-RAY DIFFRACTION 3 Å
Organisms	Chlamydomonas reinhardtii
Macromolecule	PROTEIN (I-CREI) (protein) DNA (5'-D(CPGPAPAPAPCPTPGPTPCPTPCPAPCPGPAPCPGPTPTPTPTP* GPC)-3') (nucleic acid) DNA (5'-D(GPCPAPAPAPAPCPGPTPCPGPTPGPAPGPAPCPAPGPTPTPTP CP*G)-3') (nucleic acid)
Unique Ligands	CA

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1CYQ \| pdb_00001cyq	Download File View File

INTRON ENCODED HOMING ENDONUCLEASE I-PPOI (H98A)/DNA HOMING SITE COMPLEX

Galburt, E.A., Chevalier, B., Jurica, M.S., Flick, K.E., Stoddard, B.L.

(1999) Nat Struct Biol 6: 1096-1099

Released	1999-11-19
Method	X-RAY DIFFRACTION 1.93 Å
Organisms	Physarum polycephalum
Macromolecule	INTRON-ENCODED HOMING ENDONUCLEASE I-PPOI (protein) 5'-D(TPTPGPAPCPTPCPTPCPTPTPAPAPGPAPGPAPGPTPCP*A)-3' (nucleic acid)
Unique Ligands	MG, ZN

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1CZ0 \| pdb_00001cz0	Download File View File

INTRON ENCODED HOMING ENDONUCLEASE I-PPOI/DNA COMPLEX LACKING CATALYTIC METAL ION

Galburt, E.A., Chevalier, B., Jurica, M.S., Flick, K.E., Stoddard, B.L.

(1999) Nat Struct Biol 6: 1096-1099

Released	1999-11-19
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Physarum polycephalum
Macromolecule	INTRON-ENCODED HOMING ENDONUCLEASE I-PPOI (protein) DNA (5'-D(TPTPGPAPCPTPCPTPCPTPTPAPAPGPAPGPAPGPTPCP*A)-3') (nucleic acid)
Unique Ligands	NA, ZN

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1D7P \| pdb_00001d7p	Download File View File

Crystal structure of the c2 domain of human factor viii at 1.5 a resolution at 1.5 A

Pratt, K.P., Shen, B.W., Stoddard, B.L.

(1999) Nature 402: 439-442

Released	1999-12-01
Method	X-RAY DIFFRACTION 1.5 Å
Organisms	Homo sapiens
Macromolecule	COAGULATION FACTOR VIII PRECURSOR (protein)
Unique Ligands	CYS, GOL, SO4

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1DT0 \| pdb_00001dt0	Download File View File

CLONING, SEQUENCE, AND CRYSTALLOGRAPHIC STRUCTURE OF RECOMBINANT IRON SUPEROXIDE DISMUTASE FROM PSEUDOMONAS OVALIS

Bond, C.J., Huang, J., Hajduk, R., Flick, K., Heath, P., Stoddard, B.L.

(2000) Acta Crystallogr D Biol Crystallogr 56: 1359-1366

Released	2000-12-20
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Pseudomonas putida
Macromolecule	SUPEROXIDE DISMUTASE (protein)
Unique Ligands	FE

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1EVW \| pdb_00001evw	Download File View File

L116A MUTANT OF THE HOMING ENDONUCLEASE I-PPOI COMPLEXED TO HOMING SITE DNA.

Galburt, E.A., Jurica, M.S., Chevalier, B.S., Erho, D., Stoddard, B.L.

(2000) J Mol Biology 300: 877-887

Released	2000-08-03
Method	X-RAY DIFFRACTION 3.1 Å
Organisms	Physarum polycephalum
Macromolecule	I-PPOI HOMING ENDONUCLEASE (protein) DNA (5'-D(TPGPAPCPTPCPTPCPTPTPAPA)-3') (nucleic acid) DNA (5'-D(TPGPGPCPTPAPCPCPTPTPAPA)-3') (nucleic acid) DNA (5'-D(PGPAPGPAPGPTPCPA)-3') (nucleic acid) DNA (5'-D(PGPGPTPAPGPCPCPA)-3') (nucleic acid)
Unique Ligands	MG, ZN

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1EVX \| pdb_00001evx	Download File View File

APO CRYSTAL STRUCTURE OF THE HOMING ENDONUCLEASE, I-PPOI

Galburt, E.A., Jurica, M.S., Chevalier, B.S., Erho, D., Stoddard, B.L.

(2000) J Mol Biology 300: 877-887

Released	2000-08-02
Method	X-RAY DIFFRACTION 2 Å
Organisms	Physarum polycephalum
Macromolecule	INTRON-ENCODED HOMING ENDONUCLEASE I-PPOI (protein)
Unique Ligands	SO4, ZN

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1G9Y \| pdb_00001g9y	Download File View File

HOMING ENDONUCLEASE I-CREI / DNA SUBSTRATE COMPLEX WITH CALCIUM

Chevalier, B., Monnat, R.J., Stoddard, B.L.

(2001) Nat Struct Biol 8: 312-316

Released	2001-04-02
Method	X-RAY DIFFRACTION 2.05 Å
Organisms	Chlamydomonas reinhardtii
Macromolecule	DNA ENDONUCLEASE I-CREI (protein) 5'-D(CPGPAPAPAPCPTPGPTPCPTPCPAPCPGPAPCPGPTPTPTPTPGPC)-3' (nucleic acid) 5'-D(GPCPAPAPAPAPCPGPTPCPGPTPGPAPGPAPCPAPGPTPTPTPCPG)-3' (nucleic acid)
Unique Ligands	CA

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1G9Z \| pdb_00001g9z	Download File View File

LAGLIDADG HOMING ENDONUCLEASE I-CREI / DNA PRODUCT COMPLEX WITH MAGNESIUM

Chevalier, B., Monnat, R.J., Stoddard, B.L.

(2001) Nat Struct Biol 8: 312-316

Released	2001-04-02
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Chlamydomonas reinhardtii
Macromolecule	DNA ENDONUCLEASE I-CREI (protein) 5'-D(CPGPAPAPAPCPTPGPTPCPTPCPAPC)-3' (nucleic acid) 5'-D(GPCPAPAPAPAPCPGPTPCPGPTPGPA)-3' (nucleic acid) 5'-D(PGPAPCPAPGPTPTPTPCPG)-3' (nucleic acid) 5'-D(PGPAPCPGPTPTPTPTPGPC)-3' (nucleic acid)
Unique Ligands	MG

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1IDC \| pdb_00001idc	Download File View File

ISOCITRATE DEHYDROGENASE FROM E.COLI (MUTANT K230M), STEADY-STATE INTERMEDIATE COMPLEX DETERMINED BY LAUE CRYSTALLOGRAPHY

Bolduc, J.M., Dyer, D.H., Scott, W.G., Singer, P., Sweet, R.M., Koshland Junior, D.E., Stoddard, B.L.

(1995) Science 268: 1312-1318

Released	1996-03-08
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Escherichia coli
Macromolecule	ISOCITRATE DEHYDROGENASE (protein)
Unique Ligands	MG, OXS

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1IDD \| pdb_00001idd	Download File View File

ISOCITRATE DEHYDROGENASE Y160F MUTANT APO ENZYME

Lee, M.E., Dyer, D.H., Klein, O.D., Bolduc, J.M., Stoddard, B.L., Koshland Junior, D.E.

(1995) Science 268: 1312-1318

Released	1996-03-08
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Escherichia coli
Macromolecule	ISOCITRATE DEHYDROGENASE (protein)

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1IDE \| pdb_00001ide	Download File View File

ISOCITRATE DEHYDROGENASE Y160F MUTANT STEADY-STATE INTERMEDIATE COMPLEX (LAUE DETERMINATION)

Bolduc, J.M., Dyer, D.H., Scott, W.G., Singer, P., Sweet, R.M., Koshland Junior, D.E., Stoddard, B.L.

(1995) Science 268: 1312-1318

Released	1996-03-08
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Escherichia coli
Macromolecule	ISOCITRATE DEHYDROGENASE (protein)
Unique Ligands	ICT, MG, NAP

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1IDF \| pdb_00001idf	Download File View File

ISOCITRATE DEHYDROGENASE K230M MUTANT APO ENZYME

Bolduc, J.M., Dyer, D.H., Scott, W.G., Singer, P., Sweet, R.M., Koshland Junior, D.E., Stoddard, B.L.

(1995) Science 268: 1312-1318

Released	1996-03-08
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Escherichia coli
Macromolecule	ISOCITRATE DEHYDROGENASE (protein)

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1IKA \| pdb_00001ika	Download File View File

STRUCTURE OF ISOCITRATE DEHYDROGENASE WITH ALPHA-KETOGLUTARATE AT 2.7 ANGSTROMS RESOLUTION: CONFORMATIONAL CHANGES INDUCED BY DECARBOXYLATION OF ISOCITRATE

Stoddard, B.L., Koshland Junior, D.E.

(1993) Biochemistry 32: 9317-9322

Released	1994-07-31
Method	X-RAY DIFFRACTION 2.7 Å
Organisms	Escherichia coli
Macromolecule	ISOCITRATE DEHYDROGENASE (protein)
Unique Ligands	AKG, CA

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1IPP \| pdb_00001ipp	Download File View File

HOMING ENDONUCLEASE/DNA COMPLEX

Flick, K.E., Jurica, M.S., Monnat Jr., R.J., Stoddard, B.L.

(1998) Nature 394: 96-101

Released	1998-09-02
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Physarum polycephalum
Macromolecule	INTRON-ENCODED ENDONUCLEASE I-PPOI (protein) DNA (5'-D(TPTPGPAPCPTPCPTPCPTPTPAPAPGPAPGPAPGPTPCP*A)-3') (nucleic acid)
Unique Ligands	CD, MG

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1IQD \| pdb_00001iqd	Download File View File

Human Factor VIII C2 Domain complexed to human monoclonal BO2C11 Fab.

Spiegel Jr., P.C., Jacquemin, M., Saint-Remy, J.M., Stoddard, B.L., Pratt, K.P.

(2001) Blood 98: 13-19

Released	2001-08-15
Method	X-RAY DIFFRACTION 2 Å
Organisms	Homo sapiens
Macromolecule	HUMAN FACTOR VIII (protein) HUMAN MONOCLONAL BO2C11 FAB HEAVY CHAIN (protein) HUMAN MONOCLONAL BO2C11 FAB LIGHT CHAIN (protein)