3FCS

Structure of complete ectodomain of integrin aIIBb3

PDB DOI: https://doi.org/10.2210/pdb3FCS/pdb

Classification: Cell Adhesion/BLOOD CLOTTING
Organism(s): Homo sapiens
Expression System: Cricetulus griseus
Mutation(s): Yes

Deposited: 2008-11-22 Released: 2009-01-20
Deposition Author(s): Zhu, J., Luo, B.-H., Xiao, T., Zhang, C., Nishida, N., Springer, T.A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.55 Å
R-Value Free: 0.268
R-Value Work: 0.233
R-Value Observed: 0.233

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.2 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 368.9 kDa
Atom Count: 24,961
Modelled Residue Count: 3,101
Deposited Residue Count: 3,298
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Integrin, alpha 2b	A, C	959	Homo sapiens	Mutation(s): 0 Gene Names: ITGA2B
UniProt & NIH Common Fund Data Resources
Find proteins for P08514 (Homo sapiens) Explore P08514 Go to UniProtKB: P08514
PHAROS: P08514 GTEx: ENSG00000005961
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P08514
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-3	B, D	690	Homo sapiens	Mutation(s): 1 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

Oligosaccharides

Help

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

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-3)-alpha-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
Glycosylation Resources
GlyTouCan: G48068RF GlyCosmos: G48068RF GlyGen: G48068RF

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	G	3		N-Glycosylation	Interactions Focus chain G Interactions & Density Focus chain G
Glycosylation Resources
GlyTouCan: G62182OO GlyCosmos: G62182OO GlyGen: G62182OO

Entity ID: 6
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	I	5		N-Glycosylation	Interactions Focus chain I Interactions & Density Focus chain I
Glycosylation Resources
GlyTouCan: G75436UI GlyCosmos: G75436UI GlyGen: G75436UI

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain FA [auth C] SDF format, chain T [auth A] SDF format, chain U [auth A] SDF format, chain EA [auth C] SDF format, chain OA [auth D] MOL2 format, chain FA [auth C] MOL2 format, chain T [auth A] MOL2 format, chain U [auth A] MOL2 format, chain EA [auth C] MOL2 format, chain OA [auth D]	EA [auth C], FA [auth C], OA [auth D], T [auth A], U [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain EA [auth C] Focus chain FA [auth C] Focus chain OA [auth D] Focus chain T [auth A] Focus chain U [auth A] Interactions & Density Focus chain EA [auth C] Focus chain FA [auth C] Focus chain OA [auth D] Focus chain T [auth A] Focus chain U [auth A]
IMD Query on IMD Download Ideal Coordinates CCD File SDF format, chain GA [auth C] SDF format, chain HA [auth C] SDF format, chain JA [auth C] SDF format, chain V [auth A] SDF format, chain IA [auth C] SDF format, chain KA [auth C] MOL2 format, chain GA [auth C] MOL2 format, chain HA [auth C] MOL2 format, chain JA [auth C] MOL2 format, chain V [auth A] MOL2 format, chain IA [auth C] MOL2 format, chain KA [auth C]	GA [auth C] HA [auth C] IA [auth C] JA [auth C] KA [auth C] GA [auth C], HA [auth C], IA [auth C], JA [auth C], KA [auth C], V [auth A]	IMIDAZOLE C₃ H₅ N₂ RAXXELZNTBOGNW-UHFFFAOYSA-O		Interactions Focus chain GA [auth C] Focus chain HA [auth C] Focus chain IA [auth C] Focus chain JA [auth C] Focus chain KA [auth C] Focus chain V [auth A] Interactions & Density Focus chain GA [auth C] Focus chain HA [auth C] Focus chain IA [auth C] Focus chain JA [auth C] Focus chain KA [auth C] Focus chain V [auth A]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain CA [auth C] SDF format, chain NA [auth D] SDF format, chain P [auth A] SDF format, chain R [auth A] SDF format, chain AA [auth C] SDF format, chain BA [auth C] SDF format, chain DA [auth C] SDF format, chain MA [auth D] SDF format, chain O [auth A] SDF format, chain Q [auth A] SDF format, chain S [auth A] SDF format, chain X [auth B] SDF format, chain Y [auth B] SDF format, chain Z [auth C] MOL2 format, chain CA [auth C] MOL2 format, chain NA [auth D] MOL2 format, chain P [auth A] MOL2 format, chain R [auth A] MOL2 format, chain AA [auth C] MOL2 format, chain BA [auth C] MOL2 format, chain DA [auth C] MOL2 format, chain MA [auth D] MOL2 format, chain O [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain S [auth A] MOL2 format, chain X [auth B] MOL2 format, chain Y [auth B] MOL2 format, chain Z [auth C]	AA [auth C] BA [auth C] CA [auth C] DA [auth C] MA [auth D] AA [auth C], BA [auth C], CA [auth C], DA [auth C], MA [auth D], NA [auth D], O [auth A], P [auth A], Q [auth A], R [auth A], S [auth A], X [auth B], Y [auth B], Z [auth C]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain AA [auth C] Focus chain BA [auth C] Focus chain CA [auth C] Focus chain DA [auth C] Focus chain MA [auth D] Focus chain NA [auth D] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth C] Interactions & Density Focus chain AA [auth C] Focus chain BA [auth C] Focus chain CA [auth C] Focus chain DA [auth C] Focus chain MA [auth D] Focus chain NA [auth D] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth C]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain LA [auth D] SDF format, chain W [auth B] MOL2 format, chain LA [auth D] MOL2 format, chain W [auth B]	LA [auth D], W [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain LA [auth D] Focus chain W [auth B] Interactions & Density Focus chain LA [auth D] Focus chain W [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.55 Å
R-Value Free: 0.268
R-Value Work: 0.233
R-Value Observed: 0.233
Space Group: P 4₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.3	α = 90
b = 81.3	β = 90
c = 654.623	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
AMoRE	phasing
REFMAC	refinement
XDS	data reduction
XDS	data scaling

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2009-01-20

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2009-01-20
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Refinement description, Version format compliance
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Structure summary
Version 2.1: 2021-10-20
Changes: Database references, Structure summary
Version 2.2: 2023-09-06
Changes: Data collection, Refinement description

Prepare Data

Validate Data

Deposit Data

Help and Resources

3FCS

Structure of complete ectodomain of integrin aIIBb3

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Expand

Entity ID: 2

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Expand

Entity ID: 3

Glycosylation Resources

Entity ID: 4

Glycosylation Resources

Entity ID: 5

Glycosylation Resources

Entity ID: 6

Glycosylation Resources

Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)