3EGW

The crystal structure of the NarGHI mutant NarH - C16A

Structural Biology Knowledgebase: 3EGW SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.196
  • R-Value Work: 0.175

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 3EGW

Classification: OXIDOREDUCTASE

Total Structure Weight: 228975.08

Macromolecule Entities
Molecule Chains Length Organism Details
Respiratory nitrate reductase 1 alpha chain A 1244 Escherichia coli EC#: 1.7.99.4 IUBMB
Fragment: Chain A, NarG
Mutation: F10A, D362A
Gene Name(s): narG bisD narC b1224 JW1215
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Respiratory nitrate reductase 1 beta chain B 509 Escherichia coli EC#: 1.7.99.4 IUBMB
Fragment: Chain B, NarH
Mutation: C16A
Gene Name(s): narH b1225 JW1216
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Respiratory nitrate reductase 1 gamma chain C 225 Escherichia coli EC#: 1.7.99.4 IUBMB
Fragment: Chain C, NarI
Mutation: Y77A, E78A
Gene Name(s): narI chlI b1227 JW1218
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Membrane Protein

Source: inferred by homology | Group: ALPHA-HELICAL

Subgroup Name: Oxidoreductases

Protein Name: NarGHI Nitrate Reductase A


Small Molecules
Ligands 8 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
MD1
Query on MD1

A PHOSPHORIC ACID 4-(2-AMINO-4-OXO-3,4,5,6,- TETRAHYDRO-PTERIDIN-6-YL)-2-HYDROXY-3,4-DIMERCAPTO- BUT-3-EN-YL ESTER GUANYLATE ESTER
C20 H26 N10 O13 P2 S2
IRGDLSAXQOKWLX-XHEYTWMPSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MGD
Query on MGD

A 2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,7,8A,9- TETRAHYDRO-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN- 4-ONE GUANOSINE DINUCLEOTIDE
MOLYBDOPTERIN GUANOSINE DINUCLEOTIDE (Synonym)
C20 H26 N10 O13 P2 S2
VQAGYJCYOLHZDH-ILXWUORBSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
3PH
Query on 3PH

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)
AGA
Query on AGA

C (1S)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}- 1-[(PENTANOYLOXY)METHYL]ETHYL OCTANOATE
PHOSPHATIDYL GLYCEROL (Synonym)
C19 H36 O10 P
UQSXQYRZHMGKIE-DLBZAZTESA-M
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)
6MO
Query on 6MO

A MOLYBDENUM(VI) ION
Mo
HCNGUXXTNNIKCQ-UHFFFAOYSA-N
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: 1.9 Å
  • R-Value Free: 0.196
  • R-Value Work: 0.175
  • Space Group: C 2 2 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 153.99 α = 90.00
b = 241.68 β = 90.00
c = 139.48 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2008-09-11
  • Released Date: 2010-03-02
  • Deposition author(s): Bertero, M.G., Rothery, R.A., Weiner, J.H., Strynadka, N.C.J.

Revision History

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