4HOV

DypB N246A in complex with manganese

Structural Biology Knowledgebase: 4HOV SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.195
  • R-Value Work: 0.167

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 4HOV

Classification: OXIDOREDUCTASE

Total Structure Weight: 114743.52

Macromolecule Entities
Molecule Chains Length Organism Details
DypB A, B, C 353 Rhodococcus jostii EC#: 1.11.1 IUBMB
Mutation: N246A
Gene Name(s): RHA1_ro02407

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

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

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

A, B, C MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
FMT
Query on FMT

A FORMIC ACID
C H2 O2
BDAGIHXWWSANSR-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CL
Query on CL

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

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.195
  • R-Value Work: 0.167
  • Space Group: P 32 2 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 132.96 α = 90.00
b = 132.96 β = 90.00
c = 159.50 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2012-10-22
  • Released Date: 2013-01-16
  • Deposition author(s): Grigg, J.C., Singh, R., Eltis, L.D., Murphy, M.E.P.

Revision History

  • 2013-05-01
    Type: Citation | Details: Citation update
  • 2013-01-23
    Type: Citation | Details: Citation update