1GVM

CHOLINE BINDING DOMAIN OF THE MAJOR AUTOLYSIN (C-LYTA) FROM STREPTOCOCCUS PNEUMONIAE

Structural Biology Knowledgebase: 1GVM SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.294
  • R-Value Work: 0.226

Literature

Macromolecules
Sequence Display for 1GVM

Classification: CHOLINE-BINDING DOMAIN

Total Structure Weight: 97667.52

Macromolecule Entities
Molecule Chains Length Organism Details
AUTOLYSIN A, B, C..., D, E, FA, B, C, D, E, F 136 Streptococcus pneumoniae EC#: 3.5.1.28 IUBMB
Mutation: K304R
Gene Name(s): lytA SP_1937
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

F DECYLAMINE-N,N-DIMETHYL-N-OXIDE
C12 H27 N O
ZRKZFNZPJKEWPC-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
TRS
Query on TRS

F 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
TRIS BUFFER (Synonym)
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CHT
Query on CHT

A, B, C, D, E, F CHOLINE ION
C5 H14 N O
OEYIOHPDSNJKLS-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.294
  • R-Value Work: 0.226
  • Space Group: C 1 2 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 56.72 α = 90.00
b = 85.39 β = 96.54
c = 204.14 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2002-02-15
  • Released Date: 2002-08-01
  • Deposition author(s): Fernandez-Tornero, C., Lopez, R., Garcia, E., Gimenez-Gallego, G., Romero, A.

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4