3ZDX

Integrin alphaIIB beta3 headpiece and RGD peptide complex

PDB DOI: https://doi.org/10.2210/pdb3ZDX/pdb

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

Deposited: 2012-12-03 Released: 2013-06-05
Deposition Author(s): Zhu, J.H., Zhu, J.Q., Springer, T.A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.45 Å
R-Value Free: 0.197
R-Value Work: 0.163
R-Value Observed: 0.163

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: 302.56 kDa
Atom Count: 22,433
Modelled Residue Count: 2,703
Deposited Residue Count: 2,728
Unique protein chains: 4

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
INTEGRIN ALPHA-IIB	A, C	457	Homo sapiens	Mutation(s): 0
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	472	Homo sapiens	Mutation(s): 0
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
10E5 FAB, HEAVY CHAIN	E, G [auth H]	221	Mus musculus	Mutation(s): 0
Entity Groups
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
10E5 FAB, 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 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain AA [auth B] SDF format, chain RA [auth D] MOL2 format, chain AA [auth B] MOL2 format, chain RA [auth D]	AA [auth B], RA [auth D]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain AA [auth B] Focus chain RA [auth D] Interactions & Density Focus chain AA [auth B] Focus chain RA [auth D]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain DA [auth C] SDF format, chain EA [auth C] SDF format, chain FA [auth C] SDF format, chain GA [auth C] SDF format, chain HA [auth C] SDF format, chain NA [auth D] SDF format, chain P [auth A] SDF format, chain Q [auth A] SDF format, chain SA [auth L] SDF format, chain MA [auth D] MOL2 format, chain DA [auth C] MOL2 format, chain EA [auth C] MOL2 format, chain FA [auth C] MOL2 format, chain GA [auth C] MOL2 format, chain HA [auth C] MOL2 format, chain NA [auth D] MOL2 format, chain P [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain SA [auth L] MOL2 format, chain MA [auth D]	DA [auth C] EA [auth C] FA [auth C] GA [auth C] HA [auth C] DA [auth C], EA [auth C], FA [auth C], GA [auth C], HA [auth C], MA [auth D], NA [auth D], P [auth A], Q [auth A], SA [auth L]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain DA [auth C] Focus chain EA [auth C] Focus chain FA [auth C] Focus chain GA [auth C] Focus chain HA [auth C] Focus chain MA [auth D] Focus chain NA [auth D] Focus chain P [auth A] Focus chain Q [auth A] Focus chain SA [auth L] Interactions & Density Focus chain DA [auth C] Focus chain EA [auth C] Focus chain FA [auth C] Focus chain GA [auth C] Focus chain HA [auth C] Focus chain MA [auth D] Focus chain NA [auth D] Focus chain P [auth A] Focus chain Q [auth A] Focus chain SA [auth L]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain BA [auth C] SDF format, chain CA [auth C] 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 BA [auth C] MOL2 format, chain CA [auth C] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] MOL2 format, chain V [auth B]	BA [auth C] CA [auth C] M [auth A] N [auth A] O [auth A] BA [auth C], CA [auth C], M [auth A], N [auth A], O [auth A], V [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain BA [auth C] Focus chain CA [auth C] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain V [auth B] Interactions & Density Focus chain BA [auth C] Focus chain CA [auth C] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain V [auth B]
MN Query on MN Download Ideal Coordinates CCD File SDF format, chain OA [auth D] SDF format, chain PA [auth D] SDF format, chain QA [auth D] SDF format, chain X [auth B] SDF format, chain Y [auth B] SDF format, chain Z [auth B] MOL2 format, chain OA [auth D] MOL2 format, chain PA [auth D] MOL2 format, chain QA [auth D] MOL2 format, chain X [auth B] MOL2 format, chain Y [auth B] MOL2 format, chain Z [auth B]	OA [auth D] PA [auth D] QA [auth D] X [auth B] Y [auth B] OA [auth D], PA [auth D], QA [auth D], X [auth B], Y [auth B], Z [auth B]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N		Interactions Focus chain OA [auth D] Focus chain PA [auth D] Focus chain QA [auth D] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B] Interactions & Density Focus chain OA [auth D] Focus chain PA [auth D] Focus chain QA [auth D] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain IA [auth C] SDF format, chain JA [auth C] SDF format, chain KA [auth C] SDF format, chain LA [auth C] SDF format, chain R [auth A] SDF format, chain S [auth A] SDF format, chain T [auth A] SDF format, chain U [auth A] MOL2 format, chain IA [auth C] MOL2 format, chain JA [auth C] MOL2 format, chain KA [auth C] MOL2 format, chain LA [auth C] MOL2 format, chain R [auth A] MOL2 format, chain S [auth A] MOL2 format, chain T [auth A] MOL2 format, chain U [auth A]	IA [auth C] JA [auth C] KA [auth C] LA [auth C] R [auth A] IA [auth C], JA [auth C], KA [auth C], LA [auth C], R [auth A], S [auth A], T [auth A], U [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain IA [auth C] Focus chain JA [auth C] Focus chain KA [auth C] Focus chain LA [auth C] Focus chain R [auth A] Focus chain S [auth A] Focus chain T [auth A] Focus chain U [auth A] Interactions & Density Focus chain IA [auth C] Focus chain JA [auth C] Focus chain KA [auth C] Focus chain LA [auth C] Focus chain R [auth A] Focus chain S [auth A] Focus chain T [auth A] Focus chain U [auth A]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain W [auth B] MOL2 format, chain W [auth B]	W [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain W [auth B] Interactions & Density Focus chain W [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.45 Å
R-Value Free: 0.197
R-Value Work: 0.163
R-Value Observed: 0.163
Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 259.71	α = 90
b = 144.96	β = 90
c = 104.77	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHENIX	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2013-06-05

Deposition Author(s):

Zhu, J.H.

Zhu, J.Q.

Springer, T.A.

Revision History (Full details and data files)

Version 1.0: 2013-06-05
Type: Initial release
Version 1.1: 2013-07-10
Changes: Database references
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Other, Structure summary
Version 2.1: 2023-12-20
Changes: Advisory, Data collection, Database references, Derived calculations, Refinement description, Structure summary