1OD9

N-TERMINAL OF SIALOADHESIN IN COMPLEX WITH ME-A-9-N-BENZOYL-AMINO-9-DEOXY-NEU5AC (BENZ COMPOUND)

Structural Biology Knowledgebase: 1OD9 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.253
  • R-Value Work: 0.209

Literature

Macromolecules
Sequence Display for 1OD9

Classification: LECTIN / IMMUNE SYSTEM

Total Structure Weight: 13841.69

Macromolecule Entities
Molecule Chains Length Organism Details
SIALOADHESIN A 119 Mus musculus Fragment: DOMAIN ONE, IG-LIKE V-TYPE DOMAIN, RESIDUES 20-138
Details: BOUND TO ME-A-N-BENZOYL-AMINO-9-DEOXY-NEU5AC, COORDINATE SYSTEM ORIGX ORIGX MATRIX (M) ORIGX VECTOR (V)
Gene Name(s): Siglec1 Sa Sn
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

A ME-A-N-BENZOYL-AMINO-9-DEOXY-NEU5AC
C19 H26 N2 O9
ULZLCALWUIQOMB-YRIWUQCMSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SO4
Query on SO4

A SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.253
  • R-Value Work: 0.209
  • Space Group: P 43 21 2

Unit Cell:

Length (Å) Angle (°)
a = 67.86 α = 90.00
b = 67.86 β = 90.00
c = 69.25 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2003-02-14
  • Released Date: 2003-05-16
  • Deposition author(s): Zaccai, N.R., Maenaka, K., Maenaka, T., Crocker, P.R., Brossmer, R., Kelm, S., Jones, E.Y.

Revision History

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