4UM9

Crystal structure of alpha V beta 6 with peptide

PDB DOI: https://doi.org/10.2210/pdb4UM9/pdb

Classification: IMMUNE SYSTEM
Organism(s): Homo sapiens
Expression System: Homo sapiens
Mutation(s): No

Deposited: 2014-05-15 Released: 2014-11-12
Deposition Author(s): Dong, X., Springer, T.A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.266
R-Value Work: 0.222
R-Value Observed: 0.223

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 3.1 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 250.39 kDa
Atom Count: 17,049
Modelled Residue Count: 2,110
Deposited Residue Count: 2,200
Unique protein chains: 4

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Integrin alpha-V heavy chain	A, C	604	Homo sapiens	Mutation(s): 0 Gene Names: ITGAV, MSK8, VNRA, VTNR
UniProt & NIH Common Fund Data Resources
Find proteins for P06756 (Homo sapiens) Explore P06756 Go to UniProtKB: P06756
PHAROS: P06756 GTEx: ENSG00000138448
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P06756
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Integrin beta-6	B	483	Homo sapiens	Mutation(s): 0 Gene Names: ITGB6
UniProt & NIH Common Fund Data Resources
Find proteins for P18564 (Homo sapiens) Explore P18564 Go to UniProtKB: P18564
PHAROS: P18564 GTEx: ENSG00000115221
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P18564
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Integrin beta-6	D	483	Homo sapiens	Mutation(s): 0 Gene Names: ITGB6
UniProt & NIH Common Fund Data Resources
Find proteins for P18564 (Homo sapiens) Explore P18564 Go to UniProtKB: P18564
PHAROS: P18564 GTEx: ENSG00000115221
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P18564
Sequence Annotations Expand
Reference Sequence

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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Latency-associated peptide	E, F	13	Homo sapiens	Mutation(s): 0 Gene Names: TGFB3
UniProt & NIH Common Fund Data Resources
Find proteins for P10600 (Homo sapiens) Explore P10600 Go to UniProtKB: P10600
PHAROS: P10600 GTEx: ENSG00000119699
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P10600
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	G, J, K, L, M G, J, K, L, M, P	2		N-Glycosylation	Interactions Focus chain G Focus chain J Focus chain K Focus chain L Focus chain M Focus chain P Interactions & Density Focus chain G Focus chain J Focus chain K Focus chain L Focus chain M Focus chain P
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 6
Molecule	Chains	Length	2D Diagram	Glycosylation	3D 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	H	4		N-Glycosylation	Interactions Focus chain H Interactions & Density Focus chain H
Glycosylation Resources
GlyTouCan: G22573RC GlyCosmos: G22573RC GlyGen: G22573RC

Entity ID: 7
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	I, N	6		N-Glycosylation	Interactions Focus chain I Focus chain N Interactions & Density Focus chain I Focus chain N
Glycosylation Resources
GlyTouCan: G09724ZC GlyCosmos: G09724ZC GlyGen: G09724ZC

Entity ID: 8
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	O	3		N-Glycosylation	Interactions Focus chain O Interactions & Density Focus chain O
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

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 QA [auth D] SDF format, chain RA [auth D] SDF format, chain BA [auth B] SDF format, chain CA [auth B] SDF format, chain DA [auth B] SDF format, chain KA [auth C] SDF format, chain MA [auth C] SDF format, chain SA [auth D] MOL2 format, chain QA [auth D] MOL2 format, chain RA [auth D] MOL2 format, chain BA [auth B] MOL2 format, chain CA [auth B] MOL2 format, chain DA [auth B] MOL2 format, chain KA [auth C] MOL2 format, chain MA [auth C] MOL2 format, chain SA [auth D]	BA [auth B] CA [auth B] DA [auth B] KA [auth C] MA [auth C] BA [auth B], CA [auth B], DA [auth B], KA [auth C], MA [auth C], QA [auth D], RA [auth D], SA [auth D]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain BA [auth B] Focus chain CA [auth B] Focus chain DA [auth B] Focus chain KA [auth C] Focus chain MA [auth C] Focus chain QA [auth D] Focus chain RA [auth D] Focus chain SA [auth D] Interactions & Density Focus chain BA [auth B] Focus chain CA [auth B] Focus chain DA [auth B] Focus chain KA [auth C] Focus chain MA [auth C] Focus chain QA [auth D] Focus chain RA [auth D] Focus chain SA [auth D]
MAN Query on MAN Download Ideal Coordinates CCD File SDF format, chain LA [auth C] MOL2 format, chain LA [auth C]	LA [auth C]	alpha-D-mannopyranose C₆ H₁₂ O₆ WQZGKKKJIJFFOK-PQMKYFCFSA-N		Interactions Focus chain LA [auth C] Interactions & Density Focus chain LA [auth C]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain EA [auth C] SDF format, chain FA [auth C] SDF format, chain Q [auth A] SDF format, chain R [auth A] SDF format, chain S [auth A] SDF format, chain X [auth B] MOL2 format, chain EA [auth C] MOL2 format, chain FA [auth C] MOL2 format, chain Q [auth A] MOL2 format, chain R [auth A] MOL2 format, chain S [auth A] MOL2 format, chain X [auth B]	EA [auth C] FA [auth C] Q [auth A] R [auth A] S [auth A] EA [auth C], FA [auth C], Q [auth A], R [auth A], S [auth A], X [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain EA [auth C] Focus chain FA [auth C] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A] Focus chain X [auth B] Interactions & Density Focus chain EA [auth C] Focus chain FA [auth C] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A] Focus chain X [auth B]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain AA [auth B] SDF format, chain GA [auth C] SDF format, chain HA [auth C] SDF format, chain IA [auth C] SDF format, chain JA [auth C] SDF format, chain OA [auth D] SDF format, chain PA [auth D] SDF format, chain T [auth A] SDF format, chain U [auth A] SDF format, chain V [auth A] SDF format, chain W [auth A] SDF format, chain Z [auth B] MOL2 format, chain AA [auth B] MOL2 format, chain GA [auth C] MOL2 format, chain HA [auth C] MOL2 format, chain IA [auth C] MOL2 format, chain JA [auth C] MOL2 format, chain OA [auth D] MOL2 format, chain PA [auth D] MOL2 format, chain T [auth A] MOL2 format, chain U [auth A] MOL2 format, chain V [auth A] MOL2 format, chain W [auth A] MOL2 format, chain Z [auth B]	AA [auth B] GA [auth C] HA [auth C] IA [auth C] JA [auth C] AA [auth B], GA [auth C], HA [auth C], IA [auth C], JA [auth C], OA [auth D], PA [auth D], T [auth A], U [auth A], V [auth A], W [auth A], Z [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain AA [auth B] Focus chain GA [auth C] Focus chain HA [auth C] Focus chain IA [auth C] Focus chain JA [auth C] Focus chain OA [auth D] Focus chain PA [auth D] Focus chain T [auth A] Focus chain U [auth A] Focus chain V [auth A] Focus chain W [auth A] Focus chain Z [auth B] Interactions & Density Focus chain AA [auth B] Focus chain GA [auth C] Focus chain HA [auth C] Focus chain IA [auth C] Focus chain JA [auth C] Focus chain OA [auth D] Focus chain PA [auth D] Focus chain T [auth A] Focus chain U [auth A] Focus chain V [auth A] Focus chain W [auth A] Focus chain Z [auth B]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain NA [auth D] SDF format, chain Y [auth B] MOL2 format, chain NA [auth D] MOL2 format, chain Y [auth B]	NA [auth D], Y [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain NA [auth D] Focus chain Y [auth B] Interactions & Density Focus chain NA [auth D] Focus chain Y [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.266
R-Value Work: 0.222
R-Value Observed: 0.223
Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 185.02	α = 90
b = 168.09	β = 98.95
c = 101.8	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2014-11-12

Deposition Author(s):

Dong, X.

Springer, T.A.

Revision History (Full details and data files)

Version 1.0: 2014-11-12
Type: Initial release
Version 1.1: 2014-11-19
Changes: Database references
Version 1.2: 2014-12-17
Changes: Database references
Version 1.3: 2016-03-16
Changes: Database references, Derived calculations, Other, Structure summary
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Other, Structure summary
Version 3.0: 2023-03-01
Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Polymer sequence, Source and taxonomy, Structure summary
Version 3.1: 2024-02-07
Changes: Data collection, Refinement description

Prepare Data

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Deposit Data

Help and Resources

4UM9

Crystal structure of alpha V beta 6 with peptide

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

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Entity ID: 2

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

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Entity ID: 3

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

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Entity ID: 4

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

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Entity ID: 5

Glycosylation Resources

Entity ID: 6

Glycosylation Resources

Entity ID: 7

Glycosylation Resources

Entity ID: 8

Glycosylation Resources

Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)