4K5K

Structure of bovine endothelial nitric oxide synthase heme domain in complex with ((2S, 3S)-1,3-bis((6-(2,5-dimethyl-1H-pyrrol-1-yl)-4-methylpyridin-2-yl)methoxy)-2-aminobutane

Structural Biology Knowledgebase: 4K5K SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.0 Å
  • R-Value Free: 0.217
  • R-Value Work: 0.179

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 4K5K

Classification: OXIDOREDUCTASE / OXIDOREDUCTASE INHIBITOR

Total Structure Weight: 102347.35

Macromolecule Entities
Molecule Chains Length Organism Details
Nitric oxide synthase, endothelial A, B 443 Bos taurus EC#: 1.14.13.39 IUBMB
Fragment: heme domain (UNP residues 40-482)
Mutation: C100R
Gene Name(s): NOS3 Gene View
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 6 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
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Q13
Query on Q13

A, B 6,6'-{[(2S,3S)-2-aminobutane-1,3-diyl]bis(oxymethanediyl)}bis(4- methylpyridin-2-amine)
C18 H27 N5 O2
BGQWILAWEWZMTG-BBRMVZONSA-N
Ligand Explorer
 
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
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
GOL
Query on GOL

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

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

A, B ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
Q13 Ki: 2542 nM (99) BindingDB

Ki: 2542 nM  BindingMOAD
N/A in PDBbind
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
CAS
Query on CAS
A, B L-PEPTIDE LINKING C5 H12 As N O2 S CYS

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.0 Å
  • R-Value Free: 0.217
  • R-Value Work: 0.179
  • Space Group: P 21 21 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 57.92 α = 90.00
b = 106.47 β = 90.00
c = 156.74 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2013-04-14
  • Released Date: 2013-09-18
  • Deposition author(s): Li, H., Poulos, T.L.

Revision History

  • 2013-10-02
    Type: Citation | Details: Citation update