5HDB

Integrin alphaIIbbeta3 in complex with Ro-435054

PDB DOI: https://doi.org/10.2210/pdb5HDB/pdb
Entry: 5HDB supersedes: 4Z7S

Classification: MEMBRANE PROTEIN/IMMUNE SYSTEM
Organism(s): Homo sapiens, Mus musculus
Expression System: Cricetulus griseus
Mutation(s): No

Deposited: 2016-01-05 Released: 2016-02-03
Deposition Author(s): Lin, F.Y.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free: 0.237
R-Value Work: 0.212
R-Value Observed: 0.212

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: 301.44 kDa
Atom Count: 21,895
Modelled Residue Count: 2,702
Deposited Residue Count: 2,716
Unique protein chains: 4

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Integrin alpha-IIb	A, C	454	Homo sapiens	Mutation(s): 0 Gene Names: ITGA2B, GP2B, 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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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Integrin beta-3	B, D	471	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
Monoclonal antibody 10E5 heavy chain	E, G [auth H]	219	Mus musculus	Mutation(s): 0
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Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
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Reference Sequence

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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Monoclonal antibody 10E5 light chain	F, H [auth L]	214	Mus musculus	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-3)-[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	I [auth G]	5		N-Glycosylation	Interactions Focus chain I [auth G] Interactions & Density Focus chain I [auth G]
Glycosylation Resources
GlyTouCan: G22768VO GlyCosmos: G22768VO GlyGen: G22768VO

Entity ID: 6
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	J [auth I], L [auth K]	2		N-Glycosylation	Interactions Focus chain J [auth I] Focus chain L [auth K] Interactions & Density Focus chain J [auth I] Focus chain L [auth K]
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 7
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
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	K [auth J]	4		N-Glycosylation	Interactions Focus chain K [auth J] Interactions & Density Focus chain K [auth J]
Glycosylation Resources
GlyTouCan: G81315DD GlyCosmos: G81315DD GlyGen: G81315DD

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
5YB Query on 5YB Download Ideal Coordinates CCD File SDF format, chain GA [auth D] SDF format, chain X [auth B] MOL2 format, chain GA [auth D] MOL2 format, chain X [auth B]	GA [auth D], X [auth B]	N-(4-carbamimidoylbenzoyl)-beta-alanyl-L-alpha-aspartyl-L-phenylalanine C₂₄ H₂₇ N₅ O₇ XPXOBWWMCFKOKQ-ROUUACIJSA-N		Interactions Focus chain GA [auth D] Focus chain X [auth B] Interactions & Density Focus chain GA [auth D] Focus chain X [auth B]
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain KA [auth D] SDF format, chain W [auth B] MOL2 format, chain KA [auth D] MOL2 format, chain W [auth B]	KA [auth D], W [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain KA [auth D] Focus chain W [auth B] Interactions & Density Focus chain KA [auth D] Focus chain W [auth B]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain O [auth A] SDF format, chain Z [auth C] SDF format, chain LA [auth L] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain Y [auth C] MOL2 format, chain O [auth A] MOL2 format, chain Z [auth C] MOL2 format, chain LA [auth L] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain Y [auth C]	LA [auth L] M [auth A] N [auth A] O [auth A] Y [auth C] LA [auth L], M [auth A], N [auth A], O [auth A], Y [auth C], Z [auth C]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain LA [auth L] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain Y [auth C] Focus chain Z [auth C] Interactions & Density Focus chain LA [auth L] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain Y [auth C] Focus chain Z [auth C]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain P [auth A] MOL2 format, chain P [auth A]	P [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain P [auth A] Interactions & Density Focus chain P [auth A]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain CA [auth C] SDF format, chain IA [auth D] SDF format, chain JA [auth D] SDF format, chain S [auth A] SDF format, chain V [auth B] SDF format, chain DA [auth C] 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 T [auth A] MOL2 format, chain CA [auth C] MOL2 format, chain IA [auth D] MOL2 format, chain JA [auth D] MOL2 format, chain S [auth A] MOL2 format, chain V [auth B] MOL2 format, chain DA [auth C] 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 T [auth A]	CA [auth C] DA [auth C] EA [auth C] FA [auth C] IA [auth D] CA [auth C], DA [auth C], EA [auth C], FA [auth C], IA [auth D], JA [auth D], Q [auth A], R [auth A], S [auth A], T [auth A], V [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain CA [auth C] Focus chain DA [auth C] Focus chain EA [auth C] Focus chain FA [auth C] Focus chain IA [auth D] Focus chain JA [auth D] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A] Focus chain T [auth A] Focus chain V [auth B] Interactions & Density Focus chain CA [auth C] Focus chain DA [auth C] Focus chain EA [auth C] Focus chain FA [auth C] Focus chain IA [auth D] Focus chain JA [auth D] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A] Focus chain T [auth A] Focus chain V [auth B]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain BA [auth C] MOL2 format, chain AA [auth C] MOL2 format, chain BA [auth C]	AA [auth C], BA [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain AA [auth C] Focus chain BA [auth C] Interactions & Density Focus chain AA [auth C] Focus chain BA [auth C]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain U [auth B] SDF format, chain HA [auth D] MOL2 format, chain U [auth B] MOL2 format, chain HA [auth D]	HA [auth D], U [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain HA [auth D] Focus chain U [auth B] Interactions & Density Focus chain HA [auth D] Focus chain U [auth B]

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 13
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_002217 (5YB) Query on PRD_002217	GA [auth D], X [auth B]	Ro-435054	Peptide-like / Inhibitor		Interactions Focus chain GA [auth D] Focus chain X [auth B] Interactions & Density Focus chain GA [auth D] Focus chain X [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free: 0.237
R-Value Work: 0.212
R-Value Observed: 0.212
Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 259.346	α = 90
b = 144.439	β = 90
c = 104.901	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: 2016-02-03

Deposition Author(s):

Lin, F.Y.

This entry supersedes: 4Z7S

Revision History (Full details and data files)

Version 1.0: 2016-02-03
Type: Initial release
Version 1.1: 2016-03-09
Changes: Database references
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Structure summary

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Help and Resources

5HDB

Integrin alphaIIbbeta3 in complex with Ro-435054

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: 13

Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)