9YOA | pdb_00009yoa

Crystal structure of integrin a4b1 headpiece in complex with Bio-1211 (Mn)

PDB DOI: https://doi.org/10.2210/pdb9YOA/pdb

Classification: CELL ADHESION
Organism(s): Homo sapiens, synthetic construct
Expression System: Homo sapiens
Mutation(s): No

Deposited: 2025-10-13 Released: 2026-10-21
Deposition Author(s): Monroy, M.F., Lin, F.Y., Qiao, Q.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.64 Å
R-Value Free:
0.290 (Depositor), 0.291 (DCC)
R-Value Work:
0.253 (Depositor), 0.255 (DCC)
R-Value Observed:
0.255 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Conformational landscape of integrin a4b1 and its recognition of VCAM and conformation-stabilizing small molecules

Monroy, M.F., Lin, F.Y.

To be published.

Macromolecule Content

Total Structure Weight: 125.24 kDa
Atom Count: 8,367
Modeled Residue Count: 1,048
Deposited Residue Count: 1,092
Unique protein chains: 3

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Integrin alpha-4,Integrin alpha-V heavy chain	A	597	Homo sapiens	Mutation(s): 0 Gene Names: ITGA4, CD49D, ITGAV, MSK8, VNRA, VTNR
UniProt & NIH Common Fund Data Resources
Find proteins for P13612 (Homo sapiens) Explore P13612 Go to UniProtKB: P13612
PHAROS: P13612 GTEx: ENSG00000115232
Find proteins for P06756 (Homo sapiens) Explore P06756 Go to UniProtKB: P06756
PHAROS: P06756 GTEx: ENSG00000138448
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Groups	P06756 P13612
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Integrin beta-1	B	490	Homo sapiens	Mutation(s): 0 Gene Names: ITGB1
UniProt & NIH Common Fund Data Resources
Find proteins for P05556 (Homo sapiens) Explore P05556 Go to UniProtKB: P05556
PHAROS: P05556 GTEx: ENSG00000150093
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P05556
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Bio-1211	C [auth D]	5	synthetic construct	Mutation(s): 0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain CA [auth B] SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain R [auth A] SDF format, chain S [auth A] SDF format, chain T [auth A] SDF format, chain U [auth A] SDF format, chain V [auth A] SDF format, chain Y [auth B] SDF format, chain Z [auth B] MOL2 format, chain CA [auth B] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain R [auth A] MOL2 format, chain S [auth A] MOL2 format, chain T [auth A] MOL2 format, chain U [auth A] MOL2 format, chain V [auth A] MOL2 format, chain Y [auth B] MOL2 format, chain Z [auth B] mmCIF format, chain CA [auth B] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain R [auth A] mmCIF format, chain S [auth A] mmCIF format, chain T [auth A] mmCIF format, chain U [auth A] mmCIF format, chain V [auth A] mmCIF format, chain Y [auth B] mmCIF format, chain Z [auth B]	CA [auth B] D [auth A] E [auth A] F [auth A] K [auth A] CA [auth B], D [auth A], E [auth A], F [auth A], K [auth A], L [auth A], R [auth A], S [auth A], T [auth A], U [auth A], V [auth A], Y [auth B], Z [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain CA [auth B] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain R [auth A] Focus chain S [auth A] Focus chain T [auth A] Focus chain U [auth A] Focus chain V [auth A] Focus chain Y [auth B] Focus chain Z [auth B] Interactions & Density Focus chain CA [auth B] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain R [auth A] Focus chain S [auth A] Focus chain T [auth A] Focus chain U [auth A] Focus chain V [auth A] Focus chain Y [auth B] Focus chain Z [auth B]
MAN Query on MAN Download:Ideal Coordinates CCD File SDF format, chain N [auth A] SDF format, chain O [auth A] SDF format, chain P [auth A] SDF format, chain Q [auth A] SDF format, chain X [auth A] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] MOL2 format, chain P [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain X [auth A] mmCIF format, chain N [auth A] mmCIF format, chain O [auth A] mmCIF format, chain P [auth A] mmCIF format, chain Q [auth A] mmCIF format, chain X [auth A]	N [auth A], O [auth A], P [auth A], Q [auth A], X [auth A]	alpha-D-mannopyranose C₆ H₁₂ O₆ WQZGKKKJIJFFOK-PQMKYFCFSA-N		Interactions Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain X [auth A] Interactions & Density Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain X [auth A]
BMA Query on BMA Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain M [auth A] SDF format, chain W [auth A] MOL2 format, chain G [auth A] MOL2 format, chain M [auth A] MOL2 format, chain W [auth A] mmCIF format, chain G [auth A] mmCIF format, chain M [auth A] mmCIF format, chain W [auth A]	G [auth A], M [auth A], W [auth A]	beta-D-mannopyranose C₆ H₁₂ O₆ WQZGKKKJIJFFOK-RWOPYEJCSA-N		Interactions Focus chain G [auth A] Focus chain M [auth A] Focus chain W [auth A] Interactions & Density Focus chain G [auth A] Focus chain M [auth A] Focus chain W [auth A]
MN Query on MN Download:Ideal Coordinates CCD File SDF format, chain AA [auth B] SDF format, chain BA [auth B] MOL2 format, chain AA [auth B] MOL2 format, chain BA [auth B] mmCIF format, chain AA [auth B] mmCIF format, chain BA [auth B]	AA [auth B], BA [auth B]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N		Interactions Focus chain AA [auth B] Focus chain BA [auth B] Interactions & Density Focus chain AA [auth B] Focus chain BA [auth B]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A]	H [auth A], I [auth A], J [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Interactions & Density Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A]