The structure of carbamoyl phosphate synthetase determined to 2.1 A resolution.

Thoden, J.B; Raushel, F.M; Benning, M.M; Rayment, I; Holden, H.M.

Macromolecule Content

Unique protein chains: 2

1JDB

CARBAMOYL PHOSPHATE SYNTHETASE FROM ESCHERICHIA COLI

DOI: 10.2210/pdb1jdb/pdb

Classification: LIGASE
Deposited: 1997-03-25 Released: 1998-06-17
Deposition author(s): Thoden, J.B., Holden, H.M., Wesenberg, G., Raushel, F.M., Rayment, I.
Organism: Escherichia coli
Mutation(s): 1

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.1 Å
R-Value Observed: 0.179

wwPDB Validation 3D Report Full Report

Literature

Macromolecules

Classification: LIGASE

Total Structure Weight: 647382.69

Macromolecule Entities
Molecule	Chains	Length	Organism	Details
CARBAMOYL PHOSPHATE SYNTHETASE	B, E, H, K	1073	Escherichia coli	EC#: 6.3.5.5 IUBMB Gene Name(s): carB pyrA b0033 JW0031
Metabolic Pathways Maps: Reactions: ESCHER BiGG
Protein Feature View - UniProtKB AC: P00968 UniProt Full Protein Feature View for P00968 Find similar proteins by: Sequence \| Structure Show Detailed Protein Feature View for P00968/1JDB
CARBAMOYL PHOSPHATE SYNTHETASE	C, F, I, L	382	Escherichia coli	EC#: 6.3.5.5 IUBMB Mutation: E183Q Gene Name(s): carA pyrA b0032 JW0030
Metabolic Pathways Maps: Reactions: ESCHER BiGG
Protein Feature View - UniProtKB AC: P0A6F1 UniProt Full Protein Feature View for P0A6F1 Find similar proteins by: Sequence \| Structure Show Detailed Protein Feature View for P0A6F1/1JDB

Small Molecules

Ligands 8 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions	3D Interactions
ADP Query on ADP Download SDF File Download CCD File	B, E, H, K	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N	Poseview Image of ADP in 1JDB Help Black dashed lines indicate hydrogen bonds, salt bridges, and metal interactions. Green solid line show hydrophobic interactions and green dashed lines show π-π and π-cation interactions. Source Information Interactions are determined by geometric criteria as described in K. Stierand, M. Rarey (2010), Drawing the PDB: Protein-ligand complexes in two dimensions, ACS Med. Chem. Lett., DOI: 10.1021/ml100164p. Ions and some metal complexes are excluded, as well as cases where no interaction profile could be generated. Poseview diagrams can be calculated for approximately 92% of the remaining complexes in the PDB. PoseView is developed at the Center for Bioinformatics Hamburg and jointly provided with BioSolveIT as a community service at the PDB. A stand-alone version is provided by BioSolveIT.	Ligand Explorer NGL Binding Pocket (JSmol) Electron Density (JSmol)
GLN Query on GLN Download SDF File Download CCD File	B, E, H, K	GLUTAMINE C₅ H₁₀ N₂ O₃ ZDXPYRJPNDTMRX-VKHMYHEASA-N	Poseview Image of GLN in 1JDB Help Black dashed lines indicate hydrogen bonds, salt bridges, and metal interactions. Green solid line show hydrophobic interactions and green dashed lines show π-π and π-cation interactions. Source Information Interactions are determined by geometric criteria as described in K. Stierand, M. Rarey (2010), Drawing the PDB: Protein-ligand complexes in two dimensions, ACS Med. Chem. Lett., DOI: 10.1021/ml100164p. Ions and some metal complexes are excluded, as well as cases where no interaction profile could be generated. Poseview diagrams can be calculated for approximately 92% of the remaining complexes in the PDB. PoseView is developed at the Center for Bioinformatics Hamburg and jointly provided with BioSolveIT as a community service at the PDB. A stand-alone version is provided by BioSolveIT.	Ligand Explorer NGL Binding Pocket (JSmol) Electron Density (JSmol)
ORN Query on ORN Download SDF File Download CCD File	B, E, H, K	L-ornithine C₅ H₁₂ N₂ O₂ AHLPHDHHMVZTML-BYPYZUCNSA-N	Poseview Image of ORN in 1JDB Help Black dashed lines indicate hydrogen bonds, salt bridges, and metal interactions. Green solid line show hydrophobic interactions and green dashed lines show π-π and π-cation interactions. Source Information Interactions are determined by geometric criteria as described in K. Stierand, M. Rarey (2010), Drawing the PDB: Protein-ligand complexes in two dimensions, ACS Med. Chem. Lett., DOI: 10.1021/ml100164p. Ions and some metal complexes are excluded, as well as cases where no interaction profile could be generated. Poseview diagrams can be calculated for approximately 92% of the remaining complexes in the PDB. PoseView is developed at the Center for Bioinformatics Hamburg and jointly provided with BioSolveIT as a community service at the PDB. A stand-alone version is provided by BioSolveIT.	Ligand Explorer NGL Binding Pocket (JSmol) Electron Density (JSmol)
NET Query on NET Download SDF File Download CCD File	B, E, H, K	TETRAETHYLAMMONIUM ION C₈ H₂₀ N CBXCPBUEXACCNR-UHFFFAOYSA-N	Poseview Image of NET in 1JDB Help Black dashed lines indicate hydrogen bonds, salt bridges, and metal interactions. Green solid line show hydrophobic interactions and green dashed lines show π-π and π-cation interactions. Source Information Interactions are determined by geometric criteria as described in K. Stierand, M. Rarey (2010), Drawing the PDB: Protein-ligand complexes in two dimensions, ACS Med. Chem. Lett., DOI: 10.1021/ml100164p. Ions and some metal complexes are excluded, as well as cases where no interaction profile could be generated. Poseview diagrams can be calculated for approximately 92% of the remaining complexes in the PDB. PoseView is developed at the Center for Bioinformatics Hamburg and jointly provided with BioSolveIT as a community service at the PDB. A stand-alone version is provided by BioSolveIT.	Ligand Explorer NGL Binding Pocket (JSmol) Electron Density (JSmol)
PO4 Query on PO4 Download SDF File Download CCD File	B, E, H, K	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K	Poseview Image of PO4 in 1JDB Help Black dashed lines indicate hydrogen bonds, salt bridges, and metal interactions. Green solid line show hydrophobic interactions and green dashed lines show π-π and π-cation interactions. Source Information Interactions are determined by geometric criteria as described in K. Stierand, M. Rarey (2010), Drawing the PDB: Protein-ligand complexes in two dimensions, ACS Med. Chem. Lett., DOI: 10.1021/ml100164p. Ions and some metal complexes are excluded, as well as cases where no interaction profile could be generated. Poseview diagrams can be calculated for approximately 92% of the remaining complexes in the PDB. PoseView is developed at the Center for Bioinformatics Hamburg and jointly provided with BioSolveIT as a community service at the PDB. A stand-alone version is provided by BioSolveIT.	Ligand Explorer NGL Binding Pocket (JSmol) Electron Density (JSmol)
MN Query on MN Download SDF File Download CCD File	B, E, H, K	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N	Poseview Image of MN in 1JDB Help Black dashed lines indicate hydrogen bonds, salt bridges, and metal interactions. Green solid line show hydrophobic interactions and green dashed lines show π-π and π-cation interactions. Source Information Interactions are determined by geometric criteria as described in K. Stierand, M. Rarey (2010), Drawing the PDB: Protein-ligand complexes in two dimensions, ACS Med. Chem. Lett., DOI: 10.1021/ml100164p. Ions and some metal complexes are excluded, as well as cases where no interaction profile could be generated. Poseview diagrams can be calculated for approximately 92% of the remaining complexes in the PDB. PoseView is developed at the Center for Bioinformatics Hamburg and jointly provided with BioSolveIT as a community service at the PDB. A stand-alone version is provided by BioSolveIT.	Ligand Explorer NGL Binding Pocket (JSmol) Electron Density (JSmol)
K Query on K Download SDF File Download CCD File	B, C, E, F, H, I, K, L	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N	Poseview Image of K in 1JDB Help Black dashed lines indicate hydrogen bonds, salt bridges, and metal interactions. Green solid line show hydrophobic interactions and green dashed lines show π-π and π-cation interactions. Source Information Interactions are determined by geometric criteria as described in K. Stierand, M. Rarey (2010), Drawing the PDB: Protein-ligand complexes in two dimensions, ACS Med. Chem. Lett., DOI: 10.1021/ml100164p. Ions and some metal complexes are excluded, as well as cases where no interaction profile could be generated. Poseview diagrams can be calculated for approximately 92% of the remaining complexes in the PDB. PoseView is developed at the Center for Bioinformatics Hamburg and jointly provided with BioSolveIT as a community service at the PDB. A stand-alone version is provided by BioSolveIT.	Ligand Explorer NGL Binding Pocket (JSmol) Electron Density (JSmol)
CL Query on CL Download SDF File Download CCD File	B, C, E, F, H, I, K, L	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M	Poseview Image of CL in 1JDB Help Black dashed lines indicate hydrogen bonds, salt bridges, and metal interactions. Green solid line show hydrophobic interactions and green dashed lines show π-π and π-cation interactions. Source Information Interactions are determined by geometric criteria as described in K. Stierand, M. Rarey (2010), Drawing the PDB: Protein-ligand complexes in two dimensions, ACS Med. Chem. Lett., DOI: 10.1021/ml100164p. Ions and some metal complexes are excluded, as well as cases where no interaction profile could be generated. Poseview diagrams can be calculated for approximately 92% of the remaining complexes in the PDB. PoseView is developed at the Center for Bioinformatics Hamburg and jointly provided with BioSolveIT as a community service at the PDB. A stand-alone version is provided by BioSolveIT.	Ligand Explorer NGL Binding Pocket (JSmol) Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.1 Å
R-Value Observed: 0.179
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length (Å)	Angle (°)
a = 143.80	α = 90.00
b = 167.70	β = 90.00
c = 323.00	γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots

Entry History

Deposition Data

Deposited Date: 1997-03-25
Released Date: 1998-06-17
Deposition author(s): Thoden, J.B., Holden, H.M., Wesenberg, G., Raushel, F.M., Rayment, I.

Revision History

2008-03-03
Type: Version format compliance
2011-07-13
Type: Derived calculations, Version format compliance

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