1MD2

CHOLERA TOXIN B-PENTAMER WITH DECAVALENT LIGAND BMSC-0013

Structural Biology Knowledgebase: 1MD2 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.164
  • R-Value Work: 0.125

Literature

Macromolecules
Sequence Display for 1MD2

Classification: TOXIN

Total Structure Weight: 60367.35

Macromolecule Entities
Molecule Chains Length Organism Details
CHOLERA TOXIN B SUBUNIT D, E, F, G, H 103 Vibrio cholerae Gene Name(s): ctxB toxB VC_1456
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 3 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
233
Query on 233

D, E, F [5-(3,4,5-TRIHYDROXY-6-HYDROXYMETHYL-TETRAHYDRO- PYRAN-2-YLCARBAMOYL)-PENTYL]-CARBAMIC ACID METHYL ESTER
BMSC-0013 (Synonym)
C14 H26 N2 O8
YTYAKGJMNHDUDF-UUWLPUTASA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SQ
Query on SQ

D, E 3-ETHYLAMINO-4-METHYLAMINO-CYCLOBUTANE-1,2- DIONE
SQUARIC ACID (Synonym)
C7 H12 N2 O2
FYAIPBIOBLLUAM-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CYN
Query on CYN

F CYANIDE ION
C N
XFXPMWWXUTWYJX-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
233 N/A in BindingDB
Kd: 40 nM  BindingMOAD
N/A in PDBbind
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
CSS
Query on CSS
D, E, F, G, H L-PEPTIDE LINKING C3 H7 N O2 S2 CYS

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.164
  • R-Value Work: 0.125
  • Space Group: C 1 2 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 102.12 α = 90.00
b = 66.18 β = 106.33
c = 78.22 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2002-08-06
  • Released Date: 2002-12-11
  • Deposition author(s): Zhang, Z., Merritt, E.A., Ahn, M., Roach, C., Hol, W.G.J., Fan, E.

Revision History

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