4O02

AlphaVBeta3 integrin in complex with monoclonal antibody FAB fragment.

PDB DOI: https://doi.org/10.2210/pdb4O02/pdb

Classification: PROTEIN BINDING
Organism(s): Homo sapiens, Mus musculus
Expression System: Spodoptera frugiperda
Mutation(s): No

Deposited: 2013-12-13 Released: 2014-04-02
Deposition Author(s): Mahalingam, B., van Agthoven, J., Xiong, J., Arnaout, M.A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.60 Å
R-Value Free: 0.312
R-Value Work: 0.246
R-Value Observed: 0.250

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.0 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 236.04 kDa
Atom Count: 13,526
Modelled Residue Count: 2,034
Deposited Residue Count: 2,086
Unique protein chains: 4

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Integrin alpha-V	A	962	Homo sapiens	Mutation(s): 0 Gene Names: ITGAV, MSK8, VNRA
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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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Integrin beta-3	B	692	Homo sapiens	Mutation(s): 0 Gene Names: ITGB3, GP3A
UniProt & NIH Common Fund Data Resources
Find proteins for P05106 (Homo sapiens) Explore P05106 Go to UniProtKB: P05106
PHAROS: P05106 GTEx: ENSG00000259207
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P05106
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Reference Sequence

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
17E6 light chain	C [auth L]	214	Mus musculus	Mutation(s): 0
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Reference Sequence

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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
17E6 heavy chain	D [auth H]	218	Mus musculus	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
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Reference Sequence

Oligosaccharides

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Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-mannopyranose-(1-4)-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	E [auth C]	6		N-Glycosylation	Interactions Focus chain E [auth C] Interactions & Density Focus chain E [auth C]
Glycosylation Resources
GlyTouCan: G31387PS GlyCosmos: G31387PS GlyGen: G31387PS

Entity ID: 6
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	F [auth D]	3		N-Glycosylation	Interactions Focus chain F [auth D] Interactions & Density Focus chain F [auth D]
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

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	G [auth E]	6		N-Glycosylation	Interactions Focus chain G [auth E] Interactions & Density Focus chain G [auth E]
Glycosylation Resources
GlyTouCan: G09724ZC GlyCosmos: G09724ZC GlyGen: G09724ZC

Entity ID: 8
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	H [auth F], J [auth I], K [auth J]	2		N-Glycosylation	Interactions Focus chain H [auth F] Focus chain J [auth I] Focus chain K [auth J] Interactions & Density Focus chain H [auth F] Focus chain J [auth I] Focus chain K [auth J]
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 9
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-3)-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 [auth G]	6		N-Glycosylation	Interactions Focus chain I [auth G] Interactions & Density Focus chain I [auth G]
Glycosylation Resources
GlyTouCan: G06726TJ GlyCosmos: G06726TJ GlyGen: G06726TJ

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain L [auth A] SDF format, chain S [auth B] SDF format, chain T [auth B] MOL2 format, chain L [auth A] MOL2 format, chain S [auth B] MOL2 format, chain T [auth B]	L [auth A], S [auth B], T [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain L [auth A] Focus chain S [auth B] Focus chain T [auth B] Interactions & Density Focus chain L [auth A] Focus chain S [auth B] Focus chain T [auth B]
NO3 Query on NO3 Download Ideal Coordinates CCD File SDF format, chain Q [auth A] SDF format, chain R [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain R [auth A]	Q [auth A], R [auth A]	NITRATE ION N O₃ NHNBFGGVMKEFGY-UHFFFAOYSA-N		Interactions Focus chain Q [auth A] Focus chain R [auth A] Interactions & Density Focus chain Q [auth A] Focus chain R [auth A]
MN Query on MN Download Ideal Coordinates CCD File SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain O [auth A] SDF format, chain P [auth A] SDF format, chain U [auth B] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] MOL2 format, chain P [auth A] MOL2 format, chain U [auth B]	M [auth A], N [auth A], O [auth A], P [auth A], U [auth B]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N		Interactions Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain U [auth B] Interactions & Density Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain U [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.60 Å
R-Value Free: 0.312
R-Value Work: 0.246
R-Value Observed: 0.250
Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 110.464	α = 90
b = 266.988	β = 90
c = 102.163	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHASER	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2014-04-02

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2014-04-02
Type: Initial release
Version 1.1: 2015-02-25
Changes: Database references, Derived calculations
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Structure summary

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.

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Help and Resources

4O02

AlphaVBeta3 integrin in complex with monoclonal antibody FAB fragment.

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

Entity Groups

Sequence Annotations

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Entity ID: 4

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

Entity ID: 9

Glycosylation Resources

Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)