1SIW

Crystal structure of the apomolybdo-NarGHI

Structural Biology Knowledgebase: 1SIW SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.244
  • R-Value Work: 0.203

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 1SIW

Classification: OXIDOREDUCTASE

Total Structure Weight: 229009.90

Macromolecule Entities
Molecule Chains Length Organism Details
Respiratory nitrate reductase 1 alpha chain A 1246 Escherichia coli EC#: 1.7.99.4 IUBMB
Fragment: NarG
Gene Name(s): narG bisD narC b1224 JW1215
Respiratory nitrate reductase 1 beta chain B 512 Escherichia coli EC#: 1.7.99.4 IUBMB
Fragment: NarH
Gene Name(s): narH b1225 JW1216
Respiratory nitrate reductase 1 gamma chain C 225 Escherichia coli EC#: 1.7.99.4 IUBMB
Fragment: NarI
Mutation: M1X
Gene Name(s): narI chlI b1227 JW1218

Membrane Protein

Source: mpstruc | Group: ALPHA-HELICAL

Subgroup Name: Oxidoreductases

Protein Name: NarGHI Nitrate Reductase A


Small Molecules
Ligands 5 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
3PH
Query on 3PH

A, B 1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE
PHOSPHATIDIC ACID (Synonym)
C39 H77 O8 P
YFWHNAWEOZTIPI-DIPNUNPCSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
HEM
Query on HEM

C PROTOPORPHYRIN IX CONTAINING FE
HEME (Synonym)
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
GDP
Query on GDP

A GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SF4
Query on SF4

A, B IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
F3S
Query on F3S

B FE3-S4 CLUSTER
Fe3 S4
FCXHZBQOKRZXKS-MZMDZPPWAW
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
FME
Query on FME
C L-PEPTIDE LINKING C6 H11 N O3 S MET

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.244
  • R-Value Work: 0.203
  • Space Group: C 2 2 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 154.00 α = 90.00
b = 241.28 β = 90.00
c = 140.39 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2004-03-01
  • Released Date: 2004-06-08
  • Deposition author(s): Rothery, R.A., Bertero, M.G., Cammack, R., Palak, M., Blasco, F., Strynadka, N.C., Weiner, J.H.

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4