2IVF

ETHYLBENZENE DEHYDROGENASE FROM AROMATOLEUM AROMATICUM

Structural Biology Knowledgebase: 2IVF SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.88 Å
  • R-Value Free: 0.183
  • R-Value Work: 0.148

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 2IVF

Classification: OXIDOREDUCTASE

Total Structure Weight: 178275.52

Macromolecule Entities
Molecule Chains Length Organism Details
ETHYLBENZENE DEHYDROGENASE ALPHA-SUBUNIT A 976 Aromatoleum aromaticum EC#: 1.17.99.2 IUBMB
Gene Name(s): ebdA c1A65
ETHYLBENZENE DEHYDROGENASE BETA-SUBUNIT B 352 Aromatoleum aromaticum EC#: 1.17.99.2 IUBMB
Gene Name(s): ebdB c1A63
ETHYLBENZENE DEHYDROGENASE GAMMA-SUBUNIT C 214 Aromatoleum aromaticum EC#: 1.17.99.2 IUBMB
Gene Name(s): ebdC c1A62

Small Molecules
Ligands 10 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)
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)
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)
MES
Query on MES

A 2-(N-MORPHOLINO)-ETHANESULFONIC ACID
C6 H13 N O4 S
SXGZJKUKBWWHRA-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MO
Query on MO

A MOLYBDENUM ATOM
Mo
ZOKXTWBITQBERF-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
PO4
Query on PO4

B PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
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 ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.88 Å
  • R-Value Free: 0.183
  • R-Value Work: 0.148
  • Space Group: P 1 21 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 112.53 α = 90.00
b = 67.32 β = 111.30
c = 114.76 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2006-06-13
  • Released Date: 2006-09-14
  • Deposition author(s): Kloer, D.P., Hagel, C., Heider, J., Schulz, G.E.

Revision History

  • 2011-07-13
    Type: Flag residual B-value | Details: Tagged residual B temperature factor
  • 2011-07-13
    Type: Version format compliance | Details: Compliance with PDBx exchange dictionary V4
  • 2011-07-13
    Type: Source and taxonomy | Details: Remove strain from scientific name