3K6S

Structure of integrin alphaXbeta2 ectodomain

PDB DOI: https://doi.org/10.2210/pdb3K6S/pdb

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

Deposited: 2009-10-09 Released: 2010-01-12
Deposition Author(s): Xie, C., Zhu, J., Chen, X., Mi, L., Nishida, N., Springer, T.A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.50 Å
R-Value Free: 0.335
R-Value Work: 0.297
R-Value Observed: 0.297

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.0 of the entry. See complete history.

Re-refinement Note

A newer entry is available that reflects an alternative modeling of the original data: 5ES4

Macromolecule Content

Total Structure Weight: 796.01 kDa
Atom Count: 50,187
Modelled Residue Count: 6,432
Deposited Residue Count: 7,128
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Integrin alpha-X	A, C, E, G	1,095	Homo sapiens	Mutation(s): 0 Gene Names: CD11C, ITGAX
UniProt & NIH Common Fund Data Resources
Find proteins for P20702 (Homo sapiens) Explore P20702 Go to UniProtKB: P20702
PHAROS: P20702 GTEx: ENSG00000140678
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P20702
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Integrin beta-2	B, D, F, H	687	Homo sapiens	Mutation(s): 0 Gene Names: CD18, ITGB2, MFI7
UniProt & NIH Common Fund Data Resources
Find proteins for P05107 (Homo sapiens) Explore P05107 Go to UniProtKB: P05107
PHAROS: P05107 GTEx: ENSG00000160255
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P05107
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	I, K, L, M, N I, K, L, M, N, O, Q, R, T	2		N-Glycosylation	Interactions Focus chain I Focus chain K Focus chain L Focus chain M Focus chain N Focus chain O Focus chain Q Focus chain R Focus chain T Interactions & Density Focus chain I Focus chain K Focus chain L Focus chain M Focus chain N Focus chain O Focus chain Q Focus chain R Focus chain T
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	J	5		N-Glycosylation	Interactions Focus chain J Interactions & Density Focus chain J
Glycosylation Resources
GlyTouCan: G21381MC GlyCosmos: G21381MC GlyGen: G21381MC

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	P, S	3		N-Glycosylation	Interactions Focus chain P Focus chain S Interactions & Density Focus chain P Focus chain S
Glycosylation Resources
GlyTouCan: G62182OO GlyCosmos: G62182OO GlyGen: G62182OO

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 BA [auth B] SDF format, chain DA [auth C] SDF format, chain EA [auth C] SDF format, chain IA [auth D] SDF format, chain KA [auth E] SDF format, chain LA [auth E] SDF format, chain PA [auth F] SDF format, chain RA [auth G] SDF format, chain SA [auth G] SDF format, chain V [auth A] SDF format, chain W [auth A] SDF format, chain WA [auth H] MOL2 format, chain BA [auth B] MOL2 format, chain DA [auth C] MOL2 format, chain EA [auth C] MOL2 format, chain IA [auth D] MOL2 format, chain KA [auth E] MOL2 format, chain LA [auth E] MOL2 format, chain PA [auth F] MOL2 format, chain RA [auth G] MOL2 format, chain SA [auth G] MOL2 format, chain V [auth A] MOL2 format, chain W [auth A] MOL2 format, chain WA [auth H]	BA [auth B] DA [auth C] EA [auth C] IA [auth D] KA [auth E] BA [auth B], DA [auth C], EA [auth C], IA [auth D], KA [auth E], LA [auth E], PA [auth F], RA [auth G], SA [auth G], V [auth A], W [auth A], WA [auth H]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain BA [auth B] Focus chain DA [auth C] Focus chain EA [auth C] Focus chain IA [auth D] Focus chain KA [auth E] Focus chain LA [auth E] Focus chain PA [auth F] Focus chain RA [auth G] Focus chain SA [auth G] Focus chain V [auth A] Focus chain W [auth A] Focus chain WA [auth H] Interactions & Density Focus chain BA [auth B] Focus chain DA [auth C] Focus chain EA [auth C] Focus chain IA [auth D] Focus chain KA [auth E] Focus chain LA [auth E] Focus chain PA [auth F] Focus chain RA [auth G] Focus chain SA [auth G] Focus chain V [auth A] Focus chain W [auth A] Focus chain WA [auth H]
MAN Query on MAN Download Ideal Coordinates CCD File SDF format, chain U [auth A] MOL2 format, chain U [auth A]	U [auth A]	alpha-D-mannopyranose C₆ H₁₂ O₆ WQZGKKKJIJFFOK-PQMKYFCFSA-N		Interactions Focus chain U [auth A] Interactions & Density Focus chain U [auth A]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain CA [auth B] SDF format, chain FA [auth C] SDF format, chain GA [auth C] SDF format, chain HA [auth C] SDF format, chain JA [auth D] SDF format, chain MA [auth E] SDF format, chain NA [auth E] SDF format, chain OA [auth E] SDF format, chain QA [auth F] SDF format, chain TA [auth G] SDF format, chain UA [auth G] SDF format, chain VA [auth G] SDF format, chain X [auth A] SDF format, chain XA [auth H] SDF format, chain Y [auth A] SDF format, chain Z [auth A] MOL2 format, chain CA [auth B] MOL2 format, chain FA [auth C] MOL2 format, chain GA [auth C] MOL2 format, chain HA [auth C] MOL2 format, chain JA [auth D] MOL2 format, chain MA [auth E] MOL2 format, chain NA [auth E] MOL2 format, chain OA [auth E] MOL2 format, chain QA [auth F] MOL2 format, chain TA [auth G] MOL2 format, chain UA [auth G] MOL2 format, chain VA [auth G] MOL2 format, chain X [auth A] MOL2 format, chain XA [auth H] MOL2 format, chain Y [auth A] MOL2 format, chain Z [auth A]	CA [auth B] FA [auth C] GA [auth C] HA [auth C] JA [auth D] CA [auth B], FA [auth C], GA [auth C], HA [auth C], JA [auth D], MA [auth E], NA [auth E], OA [auth E], QA [auth F], TA [auth G], UA [auth G], VA [auth G], X [auth A], XA [auth H], Y [auth A], Z [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain CA [auth B] Focus chain FA [auth C] Focus chain GA [auth C] Focus chain HA [auth C] Focus chain JA [auth D] Focus chain MA [auth E] Focus chain NA [auth E] Focus chain OA [auth E] Focus chain QA [auth F] Focus chain TA [auth G] Focus chain UA [auth G] Focus chain VA [auth G] Focus chain X [auth A] Focus chain XA [auth H] Focus chain Y [auth A] Focus chain Z [auth A] Interactions & Density Focus chain CA [auth B] Focus chain FA [auth C] Focus chain GA [auth C] Focus chain HA [auth C] Focus chain JA [auth D] Focus chain MA [auth E] Focus chain NA [auth E] Focus chain OA [auth E] Focus chain QA [auth F] Focus chain TA [auth G] Focus chain UA [auth G] Focus chain VA [auth G] Focus chain X [auth A] Focus chain XA [auth H] Focus chain Y [auth A] Focus chain Z [auth A]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain AA [auth A] MOL2 format, chain AA [auth A]	AA [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain AA [auth A] Interactions & Density Focus chain AA [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.50 Å
R-Value Free: 0.335
R-Value Work: 0.297
R-Value Observed: 0.297
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 132.095	α = 90
b = 163.561	β = 90
c = 536.911	γ = 90

Software Package:

Software Name	Purpose
MAR345dtb	data collection
SOLVE	phasing
PHENIX	refinement
XDS	data reduction
XDS	data scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2010-01-12

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2010-01-12
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2017-12-13
Changes: Advisory, Source and taxonomy
Version 1.3: 2018-06-20
Changes: Data collection
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Structure summary