4HD9

Crystal structure of native human MAdCAM-1 D1D2 domain

• PDB DOI: https://doi.org/10.2210/pdb4HD9/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens
• Expression System: Cricetulus griseus
• Mutation(s): Yes 


• Deposited: 2012-10-02 Released: 2013-01-23 
• Deposition Author(s): Springer, T., Yu, Y., Zhu, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.214 
• R-Value Work: 0.171 
• R-Value Observed: 0.175 

Literature

A Different Fold with an Integrin-Binding Loop Specialized for Flexibility in Mucosal Addressin Cell Adhesion Molecule-1

Springer, T., Yu, Y., Zhu, J., Wang, J.-H., Huang, P.-S.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 22.57 kDa 
• Atom Count: 1,888 
• Modelled Residue Count: 198 
• Deposited Residue Count: 209 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mucosal addressin cell adhesion molecule 1	A	209	Homo sapiens	Mutation(s): 1  Gene Names: MADCAM1
UniProt & NIH Common Fund Data Resources
Find proteins for Q13477 (Homo sapiens) Explore Q13477  Go to UniProtKB:  Q13477
PHAROS:  Q13477 GTEx:  ENSG00000099866
Glycosylation
Glycosylation Sites: 1		Go to GlyGen: Q13477-1

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	B [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.214 
• R-Value Work: 0.171 
• R-Value Observed: 0.175 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.476	α = 90
b = 99.988	β = 90
c = 69.668	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHASER	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-01-23 
Deposition Author(s): Springer, T., Yu, Y., Zhu, J.

Revision History  

• Version 1.0: 2013-01-23
  Type: Initial release
  
• Version 1.1: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Database references, Derived calculations, Structure summary
• Version 1.2: 2024-10-30
  Changes: Data collection, Database references, Structure summary