1E6Y

Methyl-coenzyme M reductase from Methanosarcina barkeri

Structural Biology Knowledgebase: 1E6Y SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.179
  • R-Value Work: 0.160

Literature

Macromolecules
Sequence Display for 1E6Y

Classification: OXIDOREDUCTASE

Total Structure Weight: 273157.22

Macromolecule Entities
Molecule Chains Length Organism Details
METHYL-COENZYME M REDUCTASE SUBUNIT ALPHA A, D 569 Methanosarcina barkeri EC#: 2.8.4.1 IUBMB
Gene Name(s): mcrA Mbar_A0893
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
METHYL-COENZYME M REDUCTASE I BETA SUBUNIT B, E 433 Methanosarcina barkeri EC#: 2.8.4.1 IUBMB
Gene Name(s): mcrB Mbar_A0897
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
METHYL-COENZYME M REDUCTASE SUBUNIT GAMMA C, F 247 Methanosarcina barkeri EC#: 2.8.4.1 IUBMB
Gene Name(s): mcrG Mbar_A0894
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 4 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
F43
Query on F43

A, D FACTOR 430
C42 H49 N6 Ni O13
GYTCYCYCZFADOK-AOPXNBHZDS
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
TP7
Query on TP7

A, D Coenzyme B
7-MERCAPTOHEPTANOYLTHREONINEPHOSPHATE (Synonym)
C11 H22 N O7 P S
JBJSVEVEEGOEBZ-SCZZXKLOSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
COM
Query on COM

A, D 1-THIOETHANESULFONIC ACID
C2 H6 O3 S2
ZNEWHQLOPFWXOF-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
GOL
Query on GOL

A, D GLYCEROL
2, (Synonym)
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 5 Unique
ID Chains Type Formula 2D Diagram Parent
MHS
Query on MHS
A, D L-PEPTIDE LINKING C7 H11 N3 O2 HIS
AGM
Query on AGM
A, D L-PEPTIDE LINKING C7 H17 N4 O2 ARG
GL3
Query on GL3
A, D L-PEPTIDE LINKING C2 H5 N O S GLY
SMC
Query on SMC
A, D L-PEPTIDE LINKING C4 H9 N O2 S CYS
OCS
Query on OCS
C, F L-PEPTIDE LINKING C3 H7 N O5 S CYS

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.179
  • R-Value Work: 0.160
  • Space Group: P 21 21 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 113.68 α = 90.00
b = 153.10 β = 90.00
c = 153.29 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2000-08-23
  • Released Date: 2000-10-18
  • Deposition author(s): Grabarse, W., Ermler, U.

Revision History

  • 2015-05-20
    Type: Non-polymer description | Details: FORMUL, HETNAM, HETSYN
  • 2011-11-16
    Type: Geometry validation | Details: REMARK 500
  • 2011-11-16
    Type: Non-polymer description | Details: HETSYN,FORMUL
  • 2011-11-16
    Type: Data collection | Details: REMARK 200
  • 2011-11-16
    Type: Sequence database correspondence | Details: SEQADV
  • 2011-11-16
    Type: Refinement description | Details: REMARK 3
  • 2011-11-16
    Type: Polymer description | Details: COMPND
  • 2011-11-16
    Type: Version format compliance | Details: REMARK 4
  • 2011-11-16
    Type: Biological assembly | Details: REMARK 300,REMARK 350
  • 2011-11-16
    Type: Atom nomenclature | Details: HETATM
  • 2011-11-16
    Type: Other | Details: REMARK 525,MASTER,REMARK 280
  • 2011-11-16
    Type: Source and taxonomy | Details: SOURCE
  • 2011-11-16
    Type: Function and keywords | Details: KEYWDS