1P6M

Bovine endothelial NOS heme domain with (4S)-N-(4-amino-5-[aminoethyl]aminopentyl)-N'-nitroguanidine bound

Structural Biology Knowledgebase: 1P6M SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.27 Å
  • R-Value Free: 0.278
  • R-Value Work: 0.215

Literature

Macromolecules
Sequence Display for 1P6M

Classification: OXIDOREDUCTASE

Total Structure Weight: 96819.16

Macromolecule Entities
Molecule Chains Length Organism Details
Nitric-oxide synthase, endothelial A, B 417 Bos taurus EC#: 1.14.13.39 IUBMB
Fragment: NOS HEME DOMAIN
Mutation: C100R
Gene Name(s): NOS3 Gene View
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 7 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
HEM
Query on HEM

A, B PROTOPORPHYRIN IX CONTAINING FE
HEME (Synonym)
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
DP3
Query on DP3

A, B N-{(4S)-4-AMINO-5-[(2-AMINOETHYL)AMINO]PENTYL}- N'-NITROGUANIDINE
C8 H21 N7 O2
RMSWBHUVFNFNIZ-ZETCQYMHSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
H4B
Query on H4B

A, B 5,6,7,8-TETRAHYDROBIOPTERIN
C9 H15 N5 O3
FNKQXYHWGSIFBK-RPDRRWSUSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CAC
Query on CAC

A, B CACODYLATE ION
dimethylarsinate (Synonym)
C2 H6 As O2
OGGXGZAMXPVRFZ-UHFFFAOYSA-M
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
GOL
Query on GOL

A, B GLYCEROL
2, (Synonym)
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ZN
Query on ZN

B ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ACT
Query on ACT

A, B ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
DP3 Ki: 4600 - 524000 nM (99) BindingDB

Ki: 80000 nM  BindingMOAD
N/A in PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.27 Å
  • R-Value Free: 0.278
  • R-Value Work: 0.215
  • Space Group: P 21 21 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 58.03 α = 90.00
b = 106.08 β = 90.00
c = 156.67 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2003-04-29
  • Released Date: 2004-01-13
  • Deposition author(s): Flinspach, M.L., Li, H., Jamal, J., Yang, W., Huang, H., Hah, J.-M., Gomez-Vidal, J.A., Litzinger, E.A., Silverman, R.B., Poulos, T.L.

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4
  • 2011-07-13
    Type: Non-polymer description | Details: chemical name/synonym update