2KMB

COMPLEX OF 3'-NEUAC-LEWIS-X WITH A SELECTIN-LIKE MUTANT OF MANNOSE-BINDING PROTEIN A

Structural Biology Knowledgebase: 2KMB SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.0 Å
  • R-Value Free: 0.247
  • R-Value Work: 0.190

Literature

Macromolecules
Sequence Display for 2KMB

Classification: LECTIN

Total Structure Weight: 52707.58

Macromolecule Entities
Molecule Chains Length Organism Details
MANNOSE-BINDING PROTEIN-A 1, 2, 3 149 Rattus norvegicus Fragment: CLOSTRIPAIN FRAGMENT
Mutation: A211K, S212K, H213K
Gene Name(s): Mbl1
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 7 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
SIA
Query on SIA

1, 2, 3 O-SIALIC ACID
C11 H19 N O9
SQVRNKJHWKZAKO-YRMXFSIDSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MAG
Query on MAG

1, 2 BETA-METHYL-N-ACETYL-D-GLUCOSAMINE
C9 H17 N O6
ZEVOCXOZYFLVKN-JGKVKWKGSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NAG
Query on NAG

3 N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
GAL
Query on GAL

1, 2, 3 BETA-D-GALACTOSE
C6 H12 O6
WQZGKKKJIJFFOK-FPRJBGLDSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
FUC
Query on FUC

1, 2, 3 ALPHA-L-FUCOSE
C6 H12 O5
SHZGCJCMOBCMKK-SXUWKVJYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CA
Query on CA

1, 2, 3 CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CL
Query on CL

1, 2, 3 CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.0 Å
  • R-Value Free: 0.247
  • R-Value Work: 0.190
  • Space Group: C 1 2 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 79.10 α = 90.00
b = 85.00 β = 107.10
c = 98.80 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 1996-11-07
  • Released Date: 1997-02-12
  • Deposition author(s): Ng, K.K.-S., Weis, W.I.

Revision History

  • 2011-07-13
    Type: Non-polymer description | Details: chemical name/synonym update
  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4