6NAJ

Integrin AlphaVBeta3 ectodomain bound to Hr10 variant of the 10th domain of Fibronectin.

PDB DOI: https://doi.org/10.2210/pdb6NAJ/pdb

Classification: CELL ADHESION
Organism(s): Homo sapiens
Expression System: Spodoptera, Escherichia coli
Mutation(s): No

Deposited: 2018-12-05 Released: 2019-12-11
Deposition Author(s): van Agthoven, J., Arnaout, M.A.
Funding Organization(s): National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.10 Å
R-Value Free: 0.268
R-Value Work: 0.238
R-Value Observed: 0.239

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 3.2 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 197.25 kDa
Atom Count: 13,500
Modelled Residue Count: 1,700
Deposited Residue Count: 1,734
Unique protein chains: 3

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Integrin alpha-V	A	954	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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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Integrin beta-3	B	690	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
Sequence Annotations Expand
Reference Sequence

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Fibronectin, HR10 variant	C	90	Homo sapiens	Mutation(s): 0 Gene Names: FN1, FN
UniProt & NIH Common Fund Data Resources
Find proteins for P02751 (Homo sapiens) Explore P02751 Go to UniProtKB: P02751
PHAROS: P02751 GTEx: ENSG00000115414
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P02751
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-4)-beta-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	6		N-Glycosylation	Interactions Focus chain E Interactions & Density Focus chain E
Glycosylation Resources
GlyTouCan: G93290PO GlyCosmos: G93290PO GlyGen: G93290PO

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	I	3		N-Glycosylation	Interactions Focus chain I Interactions & Density Focus chain I
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

Small Molecules

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

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
HRG Query on HRG	C	L-PEPTIDE LINKING	C₇ H₁₆ N₄ O₂		ARG

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.10 Å
R-Value Free: 0.268
R-Value Work: 0.238
R-Value Observed: 0.239
Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 129.713	α = 90
b = 129.713	β = 90
c = 308.198	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2019-12-11

Deposition Author(s):

van Agthoven, J.

Arnaout, M.A.

Funding Organization	Location	Grant Number
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)	United States	K01DK101628-04

Revision History (Full details and data files)

Version 1.0: 2019-12-11
Type: Initial release
Version 1.1: 2020-02-05
Changes: Data collection, Database references
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Structure summary
Version 3.0: 2023-02-22
Type: Coordinate replacement
Reason: Ligand geometry
Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Refinement description, Source and taxonomy, Structure summary
Version 3.1: 2023-10-25
Changes: Data collection, Refinement description
Version 3.2: 2023-11-15
Changes: Data collection, Derived calculations