1NM5

R. rubrum transhydrogenase (dI.Q132N)2(dIII)1 asymmetric complex

Structural Biology Knowledgebase: 1NM5 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.264
  • R-Value Work: 0.236

Literature

Macromolecules
Sequence Display for 1NM5

Classification: OXIDOREDUCTASE

Total Structure Weight: 104270.32

Macromolecule Entities
Molecule Chains Length Organism Details
NAD(P) transhydrogenase subunit alpha part 1 A, B 384 Rhodospirillum rubrum EC#: 1.6.1.2 IUBMB
Mutation: Q132N
Gene Name(s): pntAA nntA1 Rru_A2183
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
NAD(P) transhydrogenase subunit beta C 203 Rhodospirillum rubrum EC#: 1.6.1.2 IUBMB
Fragment: NADP-binding component
Gene Name(s): pntB nntB Rru_A2181
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

C NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE (Synonym)
C21 H28 N7 O17 P3
XJLXINKUBYWONI-NNYOXOHSSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NAD
Query on NAD

A, B NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
GOL
Query on GOL

B GLYCEROL
2, (Synonym)
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
NAD N/A in BindingDB
Kd: 20000 nM  BindingMOAD
N/A in PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.264
  • R-Value Work: 0.236
  • Space Group: P 21 21 21

Unit Cell:

Length (Å) Angle (°)
a = 71.94 α = 90.00
b = 73.89 β = 90.00
c = 205.26 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2003-01-09
  • Released Date: 2004-01-13
  • Deposition author(s): Van Boxel, G.I., Quirk, P.G., Cotton, N.P., White, S.A., Jackson, J.B.

Revision History

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