Biological Assembly 1

Protein Symmetry: Cyclic - C2 (View in 3D)

Protein Stoichiometry: Homo 2-mer - A2

Macromolecule Content

• Unique protein chains: 1

1DMJ

BOVINE ENDOTHELIAL NITRIC OXIDE SYNTHASE HEME DOMAIN COMPLEXED WITH 5,6-CYCLIC-TETRAHYDROPTERIDINE

• DOI: 10.2210/pdb1dmj/pdb

• Classification: OXIDOREDUCTASE
• Deposited: 1999-12-14 Released: 2000-12-20
• Deposition author(s): Kotsonis, P., Frohlich, L.G., Raman, C.S., Li, H., Berg, M., Gerwig, R., Groehn, V., Kang, Y., Al-Masoudi, N., Taghavi-Moghadam, S., Mohr, D., Munch, U., Schnabel, J., Martasek, P., Masters, B.S., Strobel, H., Poulos, T., Matter, H., Pfleiderer, W., Schmidt, H.H.
• Organism: Bos taurus
• Expression System: Escherichia coli
• Mutation(s): 1

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free: 0.228
• R-Value Work: 0.187

wwPDB Validation 3D Report Full Report

Literature

Macromolecules

Classification: OXIDOREDUCTASE

Total Structure Weight: 102067.66

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions	3D Interactions
HEM	A, B	PROTOPORPHYRIN IX CONTAINING FE HEME (Synonym) C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L	Poseview Image of HEM in 1DMJ 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)
AP4	A, B	7-AMINO-3,3A,4,5-TETRAHYDRO-8H-2-OXA-5,6,8,9B- TETRAAZA-CYCLOPENTA[A]NAPHTHALENE-1,9-DIONE 5,6-CYCLIC-TETRAHYDROPTERIDINE (Synonym) C8 H9 N5 O3 XAZOBOCYEGBXHD-GSVOUGTGSA-N	Poseview Image of AP4 in 1DMJ 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)
CAC	A, B	CACODYLATE ION dimethylarsinate (Synonym) C2 H6 As O2 OGGXGZAMXPVRFZ-UHFFFAOYSA-M	Poseview Image of CAC in 1DMJ 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)
ITU	A, B	ETHYLISOTHIOUREA C3 H8 N2 S VFIZBHJTOHUOEK-UHFFFAOYSA-N	Poseview Image of ITU in 1DMJ 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)
GOL	A, B	GLYCEROL 2, (Synonym) C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N	Poseview Image of GOL in 1DMJ 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)
ZN	A	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N	Poseview Image of ZN in 1DMJ 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)
ACT	A, B	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M	Poseview Image of ACT in 1DMJ 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)

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
ITU	IC50: 1300 nM (93) BindingDB N/A in BindingMoad N/A in PDBbind

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free: 0.228
• R-Value Work: 0.187
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length (Å)	Angle (°)
a = 57.90	α = 90.00
b = 106.49	β = 90.00
c = 156.55	γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots

Entry History

Deposition Data

• Deposited Date: 1999-12-14
• Released Date: 2000-12-20
• Deposition author(s): Kotsonis, P., Frohlich, L.G., Raman, C.S., Li, H., Berg, M., Gerwig, R., Groehn, V., Kang, Y., Al-Masoudi, N., Taghavi-Moghadam, S., Mohr, D., Munch, U., Schnabel, J., Martasek, P., Masters, B.S., Strobel, H., Poulos, T., Matter, H., Pfleiderer, W., Schmidt, H.H.

Revision History

• 2008-04-27
  Type: Version format compliance
• 2011-07-13
  Type: Non-polymer description, Version format compliance