4I8C

X-ray structure of NikA in complex with Ni-(L-His)2

Structural Biology Knowledgebase: 4I8C SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.234
  • R-Value Work: 0.189

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 4I8C

Classification: TRANSPORT PROTEIN

Total Structure Weight: 172106.42

Macromolecule Entities
Molecule Chains Length Organism Details
Nickel-binding periplasmic protein A, B, C 502 Escherichia coli Gene Name(s): nikA b3476 JW3441

Small Molecules
Ligands 6 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
HIS
Query on HIS

A, B, C HISTIDINE
C6 H10 N3 O2
HNDVDQJCIGZPNO-YFKPBYRVSA-O
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SO4
Query on SO4

B, C SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
GOL
Query on GOL

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

A, B, C ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NI
Query on NI

A, B, C NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CL
Query on CL

B CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.234
  • R-Value Work: 0.189
  • Space Group: P 62
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 158.63 α = 90.00
b = 158.63 β = 90.00
c = 135.82 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2012-12-03
  • Released Date: 2013-01-30
  • Deposition author(s): Lebrette, H., Iannello, M., Fontecilla-Camps, J.C., Cavazza, C.

Revision History

No revisions since initial release