4WK4

Metal Ion and Ligand Binding of Integrin

PDB DOI: https://doi.org/10.2210/pdb4WK4/pdb

Classification: CELL ADHESION/IMMUNE SYSTEM
Organism(s): Homo sapiens
Expression System: Homo sapiens
Mutation(s): No

Deposited: 2014-10-01 Released: 2014-12-03
Deposition Author(s): Xia, W., Springer, T.A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.236
R-Value Work: 0.187
R-Value Observed: 0.189

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 3.1 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 104.62 kDa
Atom Count: 7,427
Modelled Residue Count: 893
Deposited Residue Count: 903
Unique protein chains: 3

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Integrin alpha-5	A	450	Homo sapiens	Mutation(s): 0 Gene Names: ITGA5, FNRA
UniProt & NIH Common Fund Data Resources
Find proteins for P08648 (Homo sapiens) Explore P08648 Go to UniProtKB: P08648
PHAROS: P08648 GTEx: ENSG00000161638
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P08648
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Integrin beta-1	B	445	Homo sapiens	Mutation(s): 0 Gene Names: ITGB1, FNRB, MDF2, MSK12
UniProt & NIH Common Fund Data Resources
Find proteins for P05556 (Homo sapiens) Explore P05556 Go to UniProtKB: P05556
PHAROS: P05556 GTEx: ENSG00000150093
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P05556
Sequence Annotations Expand
Reference Sequence

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
ALA-CYS-ARG-GLY-ASP-GLY-TRP-CYS	C	8	Homo sapiens	Mutation(s): 0
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[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	D	6		N-Glycosylation	Interactions Focus chain D Interactions & Density Focus chain D
Glycosylation Resources
GlyTouCan: G09724ZC GlyCosmos: G09724ZC GlyGen: G09724ZC

Entity ID: 5
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	E, F	4		N-Glycosylation	Interactions Focus chain E Focus chain F Interactions & Density Focus chain E Focus chain F
Glycosylation Resources
GlyTouCan: G81315DD GlyCosmos: G81315DD GlyGen: G81315DD

Entity ID: 6
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	G, I	3		N-Glycosylation	Interactions Focus chain G Focus chain I Interactions & Density Focus chain G Focus chain I
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

Entity ID: 7
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[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	H	7		N-Glycosylation	Interactions Focus chain H Interactions & Density Focus chain H
Glycosylation Resources
GlyTouCan: G55220VL GlyCosmos: G55220VL GlyGen: G55220VL

Entity ID: 8
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	2		N/A	Interactions Focus chain J Interactions & Density Focus chain J
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain S [auth B] SDF format, chain T [auth B] SDF format, chain R [auth B] MOL2 format, chain S [auth B] MOL2 format, chain T [auth B] MOL2 format, chain R [auth B]	R [auth B], S [auth B], T [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Interactions & Density Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain Q [auth B] SDF format, chain L [auth A] SDF format, chain P [auth B] MOL2 format, chain K [auth A] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain Q [auth B] MOL2 format, chain L [auth A] MOL2 format, chain P [auth B]	K [auth A] L [auth A] M [auth A] N [auth A] P [auth B] K [auth A], L [auth A], M [auth A], N [auth A], P [auth B], Q [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain P [auth B] Focus chain Q [auth B] Interactions & Density Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain P [auth B] Focus chain Q [auth B]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain O [auth B] MOL2 format, chain O [auth B]	O [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain O [auth B] Interactions & Density Focus chain O [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.236
R-Value Work: 0.187
R-Value Observed: 0.189
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.52	α = 90
b = 112.16	β = 90
c = 169.54	γ = 90

Software Package:

Software Name	Purpose
XDS	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2014-12-03

Deposition Author(s):

Xia, W.

Springer, T.A.

Revision History (Full details and data files)

Version 1.0: 2014-12-03
Type: Initial release
Version 1.1: 2014-12-17
Changes: Database references
Version 1.2: 2014-12-24
Changes: Database references
Version 2.0: 2017-11-22
Changes: Atomic model, Database references, Derived calculations, Other, Refinement description, Source and taxonomy, Structure summary
Version 3.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Refinement description, Structure summary
Version 3.1: 2023-12-27
Changes: Data collection, Database references, Derived calculations, Structure summary