1TYE

Structural basis for allostery in integrins and binding of ligand-mimetic therapeutics to the platelet receptor for fibrinogen

PDB DOI: https://doi.org/10.2210/pdb1TYE/pdb

Classification: CELL ADHESION
Organism(s): Homo sapiens
Expression System: Cricetulus griseus
Mutation(s): No

Deposited: 2004-07-07 Released: 2004-10-12
Deposition Author(s): Xiao, T., Takagi, J., Coller, B.S., Wang, J.-H., Springer, T.A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.90 Å
R-Value Free: 0.254
R-Value Work: 0.219
R-Value Observed: 0.268

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.1 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 298.45 kDa
Atom Count: 21,019
Modelled Residue Count: 2,676
Deposited Residue Count: 2,676
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-IIb	A, C, E	452	Homo sapiens	Mutation(s): 0 Gene Names: ITGAB
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, F	440	Homo sapiens	Mutation(s): 0 Gene Names: ITGAB
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

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Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-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	G, I	4		N-Glycosylation	Interactions Focus chain G Focus chain I Interactions & Density Focus chain G Focus chain I
Glycosylation Resources
GlyTouCan: G24199JF GlyCosmos: G24199JF GlyGen: G24199JF

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	H	5		N-Glycosylation	Interactions Focus chain H Interactions & Density Focus chain H
Glycosylation Resources
GlyTouCan: G66753FB GlyCosmos: G66753FB GlyGen: G66753FB

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 DA [auth E] SDF format, chain IA [auth F] SDF format, chain JA [auth F] SDF format, chain N [auth B] SDF format, chain X [auth D] SDF format, chain O [auth B] SDF format, chain Y [auth D] MOL2 format, chain DA [auth E] MOL2 format, chain IA [auth F] MOL2 format, chain JA [auth F] MOL2 format, chain N [auth B] MOL2 format, chain X [auth D] MOL2 format, chain O [auth B] MOL2 format, chain Y [auth D]	DA [auth E] IA [auth F] JA [auth F] N [auth B] O [auth B] DA [auth E], IA [auth F], JA [auth F], N [auth B], O [auth B], X [auth D], Y [auth D]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain DA [auth E] Focus chain IA [auth F] Focus chain JA [auth F] Focus chain N [auth B] Focus chain O [auth B] Focus chain X [auth D] Focus chain Y [auth D] Interactions & Density Focus chain DA [auth E] Focus chain IA [auth F] Focus chain JA [auth F] Focus chain N [auth B] Focus chain O [auth B] Focus chain X [auth D] Focus chain Y [auth D]
CAC Query on CAC Download Ideal Coordinates CCD File SDF format, chain KA [auth F] SDF format, chain Z [auth D] SDF format, chain P [auth B] MOL2 format, chain KA [auth F] MOL2 format, chain Z [auth D] MOL2 format, chain P [auth B]	KA [auth F], P [auth B], Z [auth D]	CACODYLATE ION C₂ H₆ As O₂ OGGXGZAMXPVRFZ-UHFFFAOYSA-M		Interactions Focus chain KA [auth F] Focus chain P [auth B] Focus chain Z [auth D] Interactions & Density Focus chain KA [auth F] Focus chain P [auth B] Focus chain Z [auth D]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain BA [auth D] SDF format, chain CA [auth D] SDF format, chain GA [auth E] SDF format, chain HA [auth E] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain NA [auth F] SDF format, chain R [auth B] SDF format, chain S [auth B] SDF format, chain U [auth C] SDF format, chain V [auth C] SDF format, chain W [auth C] SDF format, chain EA [auth E] SDF format, chain FA [auth E] SDF format, chain MA [auth F] SDF format, chain T [auth C] MOL2 format, chain BA [auth D] MOL2 format, chain CA [auth D] MOL2 format, chain GA [auth E] MOL2 format, chain HA [auth E] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain NA [auth F] MOL2 format, chain R [auth B] MOL2 format, chain S [auth B] MOL2 format, chain U [auth C] MOL2 format, chain V [auth C] MOL2 format, chain W [auth C] MOL2 format, chain EA [auth E] MOL2 format, chain FA [auth E] MOL2 format, chain MA [auth F] MOL2 format, chain T [auth C]	BA [auth D] CA [auth D] EA [auth E] FA [auth E] GA [auth E] BA [auth D], CA [auth D], EA [auth E], FA [auth E], GA [auth E], HA [auth E], J [auth A], K [auth A], L [auth A], M [auth A], MA [auth F], NA [auth F], R [auth B], S [auth B], T [auth C], U [auth C], V [auth C], W [auth C]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain BA [auth D] Focus chain CA [auth D] Focus chain EA [auth E] Focus chain FA [auth E] Focus chain GA [auth E] Focus chain HA [auth E] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain MA [auth F] Focus chain NA [auth F] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth C] Focus chain U [auth C] Focus chain V [auth C] Focus chain W [auth C] Interactions & Density Focus chain BA [auth D] Focus chain CA [auth D] Focus chain EA [auth E] Focus chain FA [auth E] Focus chain GA [auth E] Focus chain HA [auth E] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain MA [auth F] Focus chain NA [auth F] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth C] Focus chain U [auth C] Focus chain V [auth C] Focus chain W [auth C]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain AA [auth D] SDF format, chain LA [auth F] SDF format, chain Q [auth B] MOL2 format, chain AA [auth D] MOL2 format, chain LA [auth F] MOL2 format, chain Q [auth B]	AA [auth D], LA [auth F], Q [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain AA [auth D] Focus chain LA [auth F] Focus chain Q [auth B] Interactions & Density Focus chain AA [auth D] Focus chain LA [auth F] Focus chain Q [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.90 Å
R-Value Free: 0.254
R-Value Work: 0.219
R-Value Observed: 0.268
Space Group: P 6₂

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 332.093	α = 90
b = 332.093	β = 90
c = 88.288	γ = 120

Software Package:

Software Name	Purpose
HKL-2000	data collection
SCALEPACK	data scaling
AMoRE	phasing
CNS	refinement
HKL-2000	data reduction

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2004-10-12

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2004-10-12
Type: Initial release
Version 1.1: 2008-04-30
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Non-polymer description, Version format compliance
Version 1.3: 2014-09-10
Changes: Database references
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Structure summary
Version 2.1: 2023-08-23
Changes: Data collection, Database references, Refinement description, Structure summary