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: Enzyme Classification Number = 6

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 4,047 Structures.

Refinements

Structure Determination Methodology

experimental (4,047)

Scientific Name of Source Organism

	Homo sapiens (1,113)
	Escherichia coli (266)
	Escherichia coli K-12 (152)
	Saccharomyces cerevisiae (104)
	Mycobacterium tuberculosis (101)
	Mycobacterium tuberculosis H37Rv (97)
	Mus musculus (85)
	Thermus thermophilus (81)
	synthetic construct (61)
	Saccharomyces cerevisiae S288C (59)

More...

Taxonomy

	Eukaryota (1,879)
	Bacteria (1,808)
	Archaea (361)
	other sequences (61)
	Duplodnaviria (33)
	Eukaryota (eukaryotes) (20)
	Riboviria (10)
	Varidnaviria (6)

Experimental Method

	X-RAY DIFFRACTION (3,658)
	ELECTRON MICROSCOPY (240)
	SOLUTION NMR (149)
	THEORETICAL MODEL (1)

Polymer Entity Type

	Protein (4,047)
	RNA (142)
	DNA (76)
	NA-hybrid (8)

Refinement Resolution (Å)

	0.5 - 1.0 (2)
	1.0 - 1.5 (165)
	1.5 - 2.0 (970)
	2.0 - 2.5 (1,384)
	2.5 - 3.0 (940)
	3.0 - 3.5 (284)
	3.5 - 4.0 (79)
	4.0 - 4.5 (27)
	> 4.5 (46)

Release Date

	1985 - 1989 (4)
	1990 - 1994 (16)
	1995 - 1999 (117)
	2000 - 2004 (310)
	2005 - 2009 (769)
	2010 - 2014 (980)
	2015 - 2019 (863)
	2020 - 2024 (956)
	2025 - 2029 (32)

Enzyme Classification Name

	Ligases (4,047)
	Transferases (1,036)
	Hydrolases (236)
	Lyases (42)
	Oxidoreductases (19)
	Isomerases (7)

Membrane Protein Annotation

	OPM (7)
	PDBTM (2)
	mpstruc (1)

Symmetry Type

	Asymmetric (2,204)
	Cyclic (1,705)
	Dihedral (331)
	Helical (3)
	Tetrahedral (1)

SCOP Classification

	Alpha and beta proteins (a+b) (878)
	Alpha and beta proteins (a/b) (965)
	Artifacts (425)
	All alpha proteins (303)
	All beta proteins (298)
	Small proteins (82)
	Multi-domain proteins (alpha and beta) (81)
	Coiled coil proteins (3)
	Peptides (3)
	Membrane and cell surface proteins and peptides (1)

AllSelected

1 to 25 of 4,047 Structures

Page 1 of 162

Sort by

Explore in 3D

11AS \| pdb_000011as	Download File View File

ASPARAGINE SYNTHETASE MUTANT C51A, C315A COMPLEXED WITH L-ASPARAGINE

Nakatsu, T., Kato, H., Oda, J.

(1998) Nat Struct Biol 5: 15-19

Released	1998-12-30
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Escherichia coli K-12
Macromolecule	ASPARAGINE SYNTHETASE (protein)
Unique Ligands	ASN

Explore in 3D

12AS \| pdb_000012as	Download File View File

ASPARAGINE SYNTHETASE MUTANT C51A, C315A COMPLEXED WITH L-ASPARAGINE AND AMP

Nakatsu, T., Kato, H., Oda, J.

(1998) Nat Struct Biol 5: 15-19

Released	1998-12-30
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Escherichia coli K-12
Macromolecule	ASPARAGINE SYNTHETASE (protein)
Unique Ligands	AMP, ASN

Explore in 3D

1A0I \| pdb_00001a0i	Download File View File

ATP-DEPENDENT DNA LIGASE FROM BACTERIOPHAGE T7 COMPLEX WITH ATP

Subramanya, H.S., Doherty, A.J., Ashford, S.R., Wigley, D.B.

(1996) Cell 85: 607-615

Released	1998-03-25
Method	X-RAY DIFFRACTION 2.6 Å
Organisms	Escherichia phage T7
Macromolecule	DNA LIGASE (protein)
Unique Ligands	ATP

Explore in 3D

1A3S \| pdb_00001a3s	Download File View File

HUMAN UBC9

Naismith, J.H., Giraud, M.

(1998) Acta Crystallogr D Biol Crystallogr 54: 891-898

Released	1998-05-27
Method	X-RAY DIFFRACTION 2.8 Å
Organisms	Homo sapiens
Macromolecule	UBC9 (protein)

Explore in 3D

1A48 \| pdb_00001a48	Download File View File

SAICAR SYNTHASE

Levdikov, V.M., Melik-Adamyan, W.R., Lamzin, V.S., Wilson, K.S.

(1998) Structure 6: 363-376

Released	1999-03-30
Method	X-RAY DIFFRACTION 1.9 Å
Organisms	Saccharomyces cerevisiae
Macromolecule	PHOSPHORIBOSYLAMINOIMIDAZOLE-SUCCINOCARBOXAMIDE SYNTHASE (protein)
Unique Ligands	SO4

Explore in 3D

1A4I \| pdb_00001a4i	Download File View File

HUMAN TETRAHYDROFOLATE DEHYDROGENASE / CYCLOHYDROLASE

Allaire, M., Li, Y., Mackenzie, R.E., Cygler, M.

(1998) Structure 6: 173-182

Released	1999-02-09
Method	X-RAY DIFFRACTION 1.5 Å
Organisms	Homo sapiens
Macromolecule	METHYLENETETRAHYDROFOLATE DEHYDROGENASE / METHENYLTETRAHYDROFOLATE CYCLOHYDROLASE (protein)
Unique Ligands	NDP

Explore in 3D

1A6X \| pdb_00001a6x	Download File View File

STRUCTURE OF THE APO-BIOTIN CARBOXYL CARRIER PROTEIN (APO-BCCP87) OF ESCHERICHIA COLI ACETYL-COA CARBOXYLASE, NMR, 49 STRUCTURES

Yao, X., Wei, D., Soden Junior, C., Summers, M.F., Beckett, D.

(1997) Biochemistry 36: 15089-15100

Released	1998-10-14
Method	SOLUTION NMR
Organisms	Escherichia coli BL21(DE3)
Macromolecule	APO-BIOTIN CARBOXYL CARRIER PROTEIN OF ACETYL-COA CARBOXYLASE (protein)

Explore in 3D

1A82 \| pdb_00001a82	Download File View File

DETHIOBIOTIN SYNTHETASE FROM ESCHERICHIA COLI, COMPLEX WITH SUBSTRATES ATP AND DIAMINOPELARGONIC ACID

Kaeck, H., Gibson, K.J., Lindqvist, Y., Schneider, G.

(1998) Proc Natl Acad Sci U S A 95: 5495-5500

Released	1999-05-11
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Escherichia coli
Macromolecule	DETHIOBIOTIN SYNTHETASE (protein)
Unique Ligands	ATP, DNN, MG

Explore in 3D

1A8H \| pdb_00001a8h	Download File View File

METHIONYL-TRNA SYNTHETASE FROM THERMUS THERMOPHILUS

Sugiura, I., Nureki, O., Ugaji, Y., Kuwabara, S., Lober, B., Giege, R., Moras, D., Yokoyama, S., Konno, M., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

(2000) Structure 8: 197-208

Released	1999-05-04
Method	X-RAY DIFFRACTION 2 Å
Organisms	Thermus thermophilus HB8
Macromolecule	METHIONYL-TRNA SYNTHETASE (protein)
Unique Ligands	ZN

Explore in 3D

1A9X \| pdb_00001a9x	Download File View File

CARBAMOYL PHOSPHATE SYNTHETASE: CAUGHT IN THE ACT OF GLUTAMINE HYDROLYSIS

Thoden, J., Holden, H.

(1998) Biochemistry 37: 8825-8831

Released	1998-10-21
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Escherichia coli
Macromolecule	CARBAMOYL PHOSPHATE SYNTHETASE (LARGE CHAIN) (protein) CARBAMOYL PHOSPHATE SYNTHETASE (SMALL CHAIN) (protein)
Unique Ligands	ADP, CL, K, MN, NET, ORN, PO4

Explore in 3D

1ADE \| pdb_00001ade	Download File View File

STRUCTURE OF ADENYLOSUCCINATE SYNTHETASE PH 7 AT 25 DEGREES CELSIUS

Silva, M.M., Poland, B.W., Hoffman, C.M., Fromm, H.J., Honzatko, R.B.

(1995) J Mol Biology 254: 431-446

Released	1996-01-29
Method	X-RAY DIFFRACTION 2 Å
Organisms	Escherichia coli
Macromolecule	ADENYLOSUCCINATE SYNTHETASE (protein)

Explore in 3D

1ADI \| pdb_00001adi	Download File View File

STRUCTURE OF ADENYLOSUCCINATE SYNTHETASE AT PH 6.5 AND 25 DEGREES CELSIUS

Silva, M.M., Poland, B.W., Hoffman, C.M., Fromm, H.J., Honzatko, R.B.

(1995) J Mol Biology 254: 431-446

Released	1996-06-10
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Escherichia coli
Macromolecule	ADENYLOSUCCINATE SYNTHETASE (protein)

Explore in 3D

1ADJ \| pdb_00001adj	Download File View File

HISTIDYL-TRNA SYNTHETASE IN COMPLEX WITH HISTIDINE

Cusack, S., Aberg, A.

(1997) Biochemistry 36: 3084-3094

Released	1997-08-20
Method	X-RAY DIFFRACTION 2.7 Å
Organisms	Thermus thermophilus
Macromolecule	HISTIDYL-TRNA SYNTHETASE (protein)
Unique Ligands	HIS, SO4

Explore in 3D

1ADY \| pdb_00001ady	Download File View File

HISTIDYL-TRNA SYNTHETASE IN COMPLEX WITH HISTIDYL-ADENYLATE

Cusack, S., Aberg, A.

(1997) Biochemistry 36: 3084-3094

Released	1997-08-20
Method	X-RAY DIFFRACTION 2.8 Å
Organisms	Thermus thermophilus
Macromolecule	HISTIDYL-TRNA SYNTHETASE (protein)
Unique Ligands	HAM, SO4

Explore in 3D

1ASY \| pdb_00001asy	Download File View File

CLASS II AMINOACYL TRANSFER RNA SYNTHETASES: CRYSTAL STRUCTURE OF YEAST ASPARTYL-TRNA SYNTHETASE COMPLEXED WITH TRNA ASP

Ruff, M., Cavarelli, J., Rees, B., Krishnaswamy, S., Thierry, J.C., Moras, D.

(1991) Science 252: 1682-1689

Released	1995-05-08
Method	X-RAY DIFFRACTION 2.9 Å
Organisms	Saccharomyces cerevisiae
Macromolecule	ASPARTYL-tRNA SYNTHETASE (protein) T-RNA (75-MER) (nucleic acid)

Explore in 3D

1ASZ \| pdb_00001asz	Download File View File

THE ACTIVE SITE OF YEAST ASPARTYL-TRNA SYNTHETASE: STRUCTURAL AND FUNCTIONAL ASPECTS OF THE AMINOACYLATION REACTION

Cavarelli, J., Rees, B., Thierry, J.C., Moras, D.

(1994) EMBO J 13: 327-337

Released	1995-05-08
Method	X-RAY DIFFRACTION 3 Å
Organisms	Saccharomyces cerevisiae
Macromolecule	ASPARTYL-tRNA SYNTHETASE (protein) T-RNA (75-MER) (nucleic acid)
Unique Ligands	ATP

Explore in 3D

1ATI \| pdb_00001ati	Download File View File

CRYSTAL STRUCTURE OF GLYCYL-TRNA SYNTHETASE FROM THERMUS THERMOPHILUS

Logan, D.T., Mazauric, M.-H., Kern, D., Moras, D.

(1995) EMBO J 14: 4156-4167

Released	1997-07-07
Method	X-RAY DIFFRACTION 2.75 Å
Organisms	Thermus thermophilus HB8
Macromolecule	GLYCYL-TRNA SYNTHETASE (protein) GLYCYL-tRNA SYNTHETASE (protein)

Explore in 3D

1AYZ \| pdb_00001ayz	Download File View File

CRYSTAL STRUCTURE OF THE SACCHAROMYCES CEREVISIAE UBIQUITIN-CONJUGATING ENZYME RAD6 (UBC2) AT 2.6A RESOLUTION

Worthylake, D.K., Prakash, S., Prakash, L., Hill, C.P.

(1998) J Biological Chem 273: 6271-6276

Released	1998-08-26
Method	X-RAY DIFFRACTION 2.6 Å
Organisms	Saccharomyces cerevisiae
Macromolecule	UBIQUITIN-CONJUGATING ENZYME RAD6 (protein)

Explore in 3D

1B04 \| pdb_00001b04	Download File View File

STRUCTURE OF THE ADENYLATION DOMAIN OF AN NAD+ DEPENDENT LIGASE

Singleton, M.R., Hakansson, K., Timson, D.J., Wigley, D.B.

(1999) Structure 7: 35-42

Released	1999-11-22
Method	X-RAY DIFFRACTION 2.8 Å
Organisms	Geobacillus stearothermophilus
Macromolecule	PROTEIN (DNA LIGASE) (protein)

Explore in 3D

1B6R \| pdb_00001b6r	Download File View File

N5-CARBOXYAMINOIMIDAZOLE RIBONUCLEOTIDE SYNTHETASE FROM E. COLI

Thoden, J.B., Kappock, T.J., Stubbe, J., Holden, H.M.

(1999) Biochemistry 38: 15480-15492

Released	1999-11-30
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Escherichia coli
Macromolecule	PROTEIN (N5-CARBOXYAMINOIMIDAZOLE RIBONUCLEOTIDE SYNTHETASE) (protein)
Unique Ligands	SO4

Explore in 3D

1B6S \| pdb_00001b6s	Download File View File

STRUCTURE OF N5-CARBOXYAMINOIMIDAZOLE RIBONUCLEOTIDE SYNTHETASE

Thoden, J.B., Kappock, T.J., Stubbe, J., Holden, H.M.

(1999) Biochemistry 38: 15480-15492

Released	1999-11-30
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Escherichia coli
Macromolecule	PROTEIN (N5-CARBOXYAMINOIMIDAZOLE RIBONUCLEOTIDE SYNTHETASE) (protein)
Unique Ligands	ADP, MG

Explore in 3D

1B70 \| pdb_00001b70	Download File View File

PHENYLALANYL TRNA SYNTHETASE COMPLEXED WITH PHENYLALANINE

Reshetnikova, L., Moor, N., Lavrik, O., Vassylyev, D.G.

(1999) J Mol Biology 287: 555-568

Released	2000-02-09
Method	X-RAY DIFFRACTION 2.7 Å
Organisms	Thermus thermophilus
Macromolecule	PHENYLALANYL-TRNA SYNTHETASE (protein)
Unique Ligands	MG, PHE

Explore in 3D

1B76 \| pdb_00001b76	Download File View File

GLYCYL-TRNA SYNTHETASE FROM THERMUS THERMOPHILUS COMPLEXED WITH ATP

Arnez, J.G., Moras, D.

(1999) J Mol Biology 286: 1449-1459

Released	1999-01-28
Method	X-RAY DIFFRACTION 3.4 Å
Organisms	Thermus thermophilus HB8
Macromolecule	Glycine--tRNA ligase (protein)
Unique Ligands	ATP

Explore in 3D

1B7Y \| pdb_00001b7y	Download File View File

PHENYLALANYL TRNA SYNTHETASE COMPLEXED WITH PHENYLALANINYL-ADENYLATE

Reshetnikova, L., Moor, N., Lavrik, O., Vassylyev, D.G.

(1999) J Mol Biology 287: 555-568

Released	2000-01-26
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Thermus thermophilus
Macromolecule	PROTEIN (PHENYLALANYL-TRNA SYNTHETASE) (protein)
Unique Ligands	FYA, MG

Explore in 3D

1B8A \| pdb_00001b8a	Download File View File

ASPARTYL-TRNA SYNTHETASE

Schmitt, E., Moulinier, L., Thierry, J.-C., Moras, D.

(1998) EMBO J 17: 5227-5237

Released	1999-02-02
Method	X-RAY DIFFRACTION 1.9 Å
Organisms	Thermococcus kodakarensis KOD1
Macromolecule	PROTEIN (ASPARTYL-TRNA SYNTHETASE) (protein)
Unique Ligands	ATP, MN

1 to 25 of 4,047 Structures

Page 1 of 162

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

11AS | pdb_000011as

12AS | pdb_000012as

1A0I | pdb_00001a0i

1A3S | pdb_00001a3s

1A48 | pdb_00001a48

1A4I | pdb_00001a4i

1A6X | pdb_00001a6x

1A82 | pdb_00001a82

1A8H | pdb_00001a8h

1A9X | pdb_00001a9x

1ADE | pdb_00001ade

1ADI | pdb_00001adi

1ADJ | pdb_00001adj

1ADY | pdb_00001ady

1ASY | pdb_00001asy

1ASZ | pdb_00001asz

1ATI | pdb_00001ati

1AYZ | pdb_00001ayz

1B04 | pdb_00001b04

1B6R | pdb_00001b6r

1B6S | pdb_00001b6s

1B70 | pdb_00001b70

1B76 | pdb_00001b76

1B7Y | pdb_00001b7y

1B8A | pdb_00001b8a