1NJF

Nucleotide bound form of an isolated E. coli clamp loader gamma subunit

Structural Biology Knowledgebase: 1NJF SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.248
  • R-Value Work: 0.210

Literature

Macromolecules
Sequence Display for 1NJF

Classification: TRANSFERASE

Total Structure Weight: 112256.89

Macromolecule Entities
Molecule Chains Length Organism Details
DNA polymerase III subunit gamma A, B, C, D 250 Escherichia coli EC#: 2.7.7.7 IUBMB
Fragment: N-terminal domains 1 and 2
Gene Name(s): dnaX dnaZ dnaZX b0470 JW0459
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

A, B, D PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
ATP-GAMMA-S; ADENOSINE 5'-(3-THIOTRIPHOSPHATE); ADENOSINE 5'- (GAMMA-THIOTRIPHOSPHATE); ADENOSINE-5'-DIPHOSPHATE MONOTHIOPHOSPHATE (Synonym)
C10 H16 N5 O12 P3 S
NLTUCYMLOPLUHL-KQYNXXCUSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ADP
Query on ADP

C ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ZN
Query on ZN

A, B, C, D ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
ADP N/A in BindingDB
Kd: 1030 nM  BindingMOAD
Kd: 1030 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.248
  • R-Value Work: 0.210
  • Space Group: P 21 21 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 71.71 α = 90.00
b = 113.35 β = 90.00
c = 121.36 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2002-12-30
  • Released Date: 2003-04-08
  • Deposition author(s): Podobnik, M., Weitze, T.F., O'Donnell, M., Kuriyan, J.

Revision History

  • 2012-03-07
    Type: Non-polymer description | Details: --
  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4