Biological Assembly 1

Protein Symmetry: Dihedral - D2 (View in 3D)

Protein Stoichiometry: Hetero 8-mer - A4B4

Biological Assembly 2

Protein Symmetry: C1 (View in 3D)

Protein Stoichiometry: AB

Biological Assembly 3

Protein Symmetry: C1 (View in 3D)

Protein Stoichiometry: AB

Biological Assembly 4

Protein Symmetry: C1 (View in 3D)

Protein Stoichiometry: AB

Biological Assembly 5

Protein Symmetry: C1 (View in 3D)

Protein Stoichiometry: AB

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

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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

Small Molecules

Ligands 8 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions	3D Interactions
ADP	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	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	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	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	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	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	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	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

• Version 1_0: 1998-06-17
  

  Type: Initial release

• Version 1_1: 2008-03-03
  

  Type: Version format compliance

• Version 1_2: 2011-07-13
  

  Type: Derived calculations, Version format compliance