9YO6 | pdb_00009yo6

Crystal structure of integrin a4b1 headpiece in complex with DS 13g (Mn)

PDB DOI: https://doi.org/10.2210/pdb9YO6/pdb

Classification: CELL ADHESION
Organism(s): Homo sapiens
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: 2.22 Å
R-Value Free:
0.258 (Depositor), 0.265 (DCC)
R-Value Work:
0.233 (Depositor), 0.239 (DCC)
R-Value Observed:
0.234 (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: 123.11 kDa
Atom Count: 8,327
Modeled Residue Count: 1,037
Deposited Residue Count: 1,087
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Integrin a4	A	597	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
Glycosylation
Glycosylation Sites: 3	Glycosylation Focus chain A
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, FNRB, MDF2, MSK12
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
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain B	Go to GlyGen: P05556-1
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C, D [auth E]	3		N-Glycosylation	Interactions Focus chain C Focus chain D [auth E] Interactions & Density Focus chain C Focus chain D [auth E]

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1CYS Query on A1CYS Download:Ideal Coordinates CCD File SDF format, chain P [auth B] MOL2 format, chain P [auth B] mmCIF format, chain P [auth B]	P [auth B]	(4-{[(2S)-1-({4-[(2-methylphenyl)carbamamido]phenyl}acetyl)pyrrolidin-2-yl]methyl}piperazin-1-yl)acetic acid C₂₇ H₃₅ N₅ O₄ AUNZHLFQXIZEJK-QHCPKHFHSA-N		Interactions Focus chain P [auth B] Interactions & Density Focus chain P [auth B]
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain O [auth B] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain O [auth B] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain O [auth B]	H [auth A], I [auth A], J [auth A], K [auth A], O [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain O [auth B] Interactions & Density Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain O [auth B]
MN Query on MN Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain L [auth B] SDF format, chain M [auth B] SDF format, chain N [auth B] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain L [auth B] mmCIF format, chain M [auth B] mmCIF format, chain N [auth B]	E [auth A] F [auth A] G [auth A] L [auth B] M [auth B] E [auth A], F [auth A], G [auth A], L [auth B], M [auth B], N [auth B]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B]