4HBQ | pdb_00004hbq

Crystal structure of a loop deleted mutant of Human MAdCAM-1 D1D2

• PDB DOI: https://doi.org/10.2210/pdb4HBQ/pdb

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


• Deposited: 2012-09-28 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: 1.40 Å
• R-Value Free: 
  0.178 (Depositor), 0.177 (DCC) 
• R-Value Work: 
  0.143 (Depositor), 0.143 (DCC) 
• R-Value Observed: 
  0.144 (Depositor) 

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.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 3 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 43.91 kDa 
• Atom Count: 4,136 
• Modeled Residue Count: 412 
• Deposited Residue Count: 412 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mucosal addressin cell adhesion molecule 1	A, B	206	Homo sapiens	Mutation(s): 2  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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	F [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
SO4	C [auth A], E [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	D [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free:  0.178 (Depositor), 0.177 (DCC) 
• R-Value Work:  0.143 (Depositor), 0.143 (DCC) 
• R-Value Observed: 0.144 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.32	α = 90
b = 69.7	β = 90
c = 101.2	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHASER	phasing
PHENIX	refinement
XDS	data reduction
SCALA	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: Advisory, Data collection, Database references, Derived calculations, Structure summary
• Version 1.2: 2021-05-26
  Changes: Source and taxonomy, Structure summary
• Version 1.3: 2024-11-20
  Changes: Advisory, Data collection, Database references, Structure summary