3ZE1

Integrin alphaIIB beta3 headpiece and RGD peptide complex

PDB DOI: https://doi.org/10.2210/pdb3ZE1/pdb

Classification: CELL ADHESION/IMMUNE SYSTEM/PEPTIDE
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: 3.00 Å
R-Value Free: 0.233
R-Value Work: 0.175
R-Value Observed: 0.176

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: 302.35 kDa
Atom Count: 21,362
Modelled Residue Count: 2,713
Deposited Residue Count: 2,740
Unique protein chains: 5

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
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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
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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, J [auth L]	214	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: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
RGD PEPTIDE	H [auth I], I [auth J]	6	Homo sapiens	Mutation(s): 0
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Reference Sequence

Oligosaccharides

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Entity ID: 6
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 G], M	4		N-Glycosylation	Interactions Focus chain K [auth G] Focus chain M Interactions & Density Focus chain K [auth G] Focus chain M
Glycosylation Resources
GlyTouCan: G81315DD GlyCosmos: G81315DD GlyGen: G81315DD

Entity ID: 7
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	L [auth K], N	2		N-Glycosylation	Interactions Focus chain L [auth K] Focus chain N Interactions & Density Focus chain L [auth K] Focus chain N
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG 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]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain GA [auth D] Focus chain X [auth B] Interactions & Density Focus chain GA [auth D] Focus chain X [auth B]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain O [auth A] SDF format, chain HA [auth L] SDF format, chain P [auth A] MOL2 format, chain O [auth A] MOL2 format, chain HA [auth L] MOL2 format, chain P [auth A]	HA [auth L], O [auth A], P [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain HA [auth L] Focus chain O [auth A] Focus chain P [auth A] Interactions & Density Focus chain HA [auth L] Focus chain O [auth A] Focus chain P [auth A]
MN Query on MN Download Ideal Coordinates CCD File SDF format, chain DA [auth D] SDF format, chain EA [auth D] SDF format, chain V [auth B] SDF format, chain W [auth B] SDF format, chain FA [auth D] SDF format, chain U [auth B] MOL2 format, chain DA [auth D] MOL2 format, chain EA [auth D] MOL2 format, chain V [auth B] MOL2 format, chain W [auth B] MOL2 format, chain FA [auth D] MOL2 format, chain U [auth B]	DA [auth D] EA [auth D] FA [auth D] U [auth B] V [auth B] DA [auth D], EA [auth D], FA [auth D], U [auth B], V [auth B], W [auth B]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N		Interactions Focus chain DA [auth D] Focus chain EA [auth D] Focus chain FA [auth D] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B] Interactions & Density Focus chain DA [auth D] Focus chain EA [auth D] Focus chain FA [auth D] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain CA [auth C] SDF format, chain Q [auth A] SDF format, chain R [auth A] SDF format, chain Z [auth C] SDF format, chain BA [auth C] SDF format, chain S [auth A] SDF format, chain T [auth A] MOL2 format, chain AA [auth C] MOL2 format, chain CA [auth C] MOL2 format, chain Q [auth A] MOL2 format, chain R [auth A] MOL2 format, chain Z [auth C] MOL2 format, chain BA [auth C] MOL2 format, chain S [auth A] MOL2 format, chain T [auth A]	AA [auth C] BA [auth C] CA [auth C] Q [auth A] R [auth A] AA [auth C], BA [auth C], CA [auth C], Q [auth A], R [auth A], S [auth A], T [auth A], 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 Q [auth A] Focus chain R [auth A] Focus chain S [auth A] Focus chain T [auth A] Focus chain Z [auth C] Interactions & Density Focus chain AA [auth C] Focus chain BA [auth C] Focus chain CA [auth C] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A] Focus chain T [auth A] Focus chain Z [auth C]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain Y [auth C] MOL2 format, chain Y [auth C]	Y [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain Y [auth C] Interactions & Density Focus chain Y [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.00 Å
R-Value Free: 0.233
R-Value Work: 0.175
R-Value Observed: 0.176
Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 258.97	α = 90
b = 144.56	β = 90
c = 104.7	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, Refinement description, Structure summary

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Help and Resources

3ZE1

Integrin alphaIIB beta3 headpiece and RGD peptide complex

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

Sequence Annotations

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Entity ID: 6

Glycosylation Resources

Entity ID: 7

Glycosylation Resources

Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)