9YO8 | pdb_00009yo8

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

PDB DOI: https://doi.org/10.2210/pdb9YO8/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: 2.53 Å
R-Value Free:
0.264 (Depositor), 0.271 (DCC)
R-Value Work:
0.224 (Depositor), 0.230 (DCC)
R-Value Observed:
0.226 (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: 122.89 kDa
Atom Count: 8,318
Modeled Residue Count: 1,043
Deposited Residue Count: 1,078
Unique protein chains: 2

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	588	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
Glycosylation
Glycosylation Sites: 4	Glycosylation Focus chain A	Go to GlyGen: P13612-1 P06756-1
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: 2	Glycosylation Focus chain B	Go to GlyGen: P05556-1
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

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	3		N-Glycosylation	Interactions Focus chain C Interactions & Density Focus chain C

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

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	F	4		N-Glycosylation	Interactions Focus chain F Interactions & Density Focus chain F

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1CYV Query on A1CYV Download:Ideal Coordinates CCD File SDF format, chain Q [auth B] MOL2 format, chain Q [auth B] mmCIF format, chain Q [auth B]	Q [auth B]	{1-[(3S)-4-({4-[(2-methylphenyl)carbamamido]phenyl}acetyl)morpholine-3-carbonyl]piperidin-4-yl}acetic acid C₂₈ H₃₄ N₄ O₆ ITXAAOWFOURIHK-DEOSSOPVSA-N		Interactions Focus chain Q [auth B] Interactions & Density Focus chain Q [auth B]
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain K [auth A] SDF format, chain L [auth B] SDF format, chain P [auth B] MOL2 format, chain G [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth B] MOL2 format, chain P [auth B] mmCIF format, chain G [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [auth B] mmCIF format, chain P [auth B]	G [auth A], K [auth A], L [auth B], P [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain G [auth A] Focus chain K [auth A] Focus chain L [auth B] Focus chain P [auth B] Interactions & Density Focus chain G [auth A] Focus chain K [auth A] Focus chain L [auth B] Focus chain P [auth B]
MN Query on MN Download:Ideal Coordinates CCD File SDF format, chain M [auth B] SDF format, chain N [auth B] SDF format, chain O [auth B] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] mmCIF format, chain M [auth B] mmCIF format, chain N [auth B] mmCIF format, chain O [auth B]	M [auth B], N [auth B], O [auth B]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N		Interactions Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Interactions & Density Focus chain M [auth B] Focus chain N [auth B] Focus chain O [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]