3K71
Structure of integrin alphaX beta2 ectodomain
- PDB DOI: https://doi.org/10.2210/pdb3K71/pdb
- Classification: CELL ADHESION
- Organism(s): Homo sapiens
- Expression System: Cricetulus griseus
- Mutation(s): No 
- Deposited: 2009-10-11 Released: 2010-01-12 
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 3.95 Å
- R-Value Free: 0.373 
- R-Value Work: 0.350 
- R-Value Observed: 0.350 
This is version 2.1 of the entry. See complete history. 
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
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Molecule | Chains | Sequence Length | Organism | Details | Image |
Integrin alpha-X | 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 AnnotationsExpand | |||||
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Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 2 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
Integrin beta-2 | 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 AnnotationsExpand | |||||
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Oligosaccharides
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, M, N, P, S | 2 | N-Glycosylation | ||
Glycosylation Resources | |||||
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT |
Entity ID: 4 | |||||
---|---|---|---|---|---|
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 | J, K, L, O, Q J, K, L, O, Q, R, U | 3 | N-Glycosylation | ||
Glycosylation Resources | |||||
GlyTouCan:  G62182OO GlyCosmos:  G62182OO GlyGen:  G62182OO |
Entity ID: 5 | |||||
---|---|---|---|---|---|
Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
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 | T | 4 | N-Glycosylation | ||
Glycosylation Resources | |||||
GlyTouCan:  G04854NQ GlyCosmos:  G04854NQ GlyGen:  G04854NQ |
Small Molecules
Ligands 3 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
NAG Query on NAG | AA [auth B] CA [auth C] DA [auth C] HA [auth D] IA [auth D] | 2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N | |||
CA Query on CA | AB [auth H] BA [auth B] EA [auth C] FA [auth C] GA [auth C] | CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N | |||
MG Query on MG | XA [auth G] | MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 3.95 Å
- R-Value Free: 0.373 
- R-Value Work: 0.350 
- R-Value Observed: 0.350 
- Space Group: P 21 21 21
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 149.664 | α = 90 |
b = 165.745 | β = 90 |
c = 537.676 | γ = 90 |
Software Name | Purpose |
---|---|
MAR345dtb | data collection |
PHASER | phasing |
PHENIX | refinement |
XDS | data reduction |
XDS | data scaling |
Entry History 
Deposition Data
- Released Date: 2010-01-12  Deposition Author(s): Xie, C., Zhu, J., Chen, X., Mi, L., Nishida, N., Springer, T.A.
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 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Structure summary - Version 2.1: 2023-09-06
Changes: Data collection, Database references, Refinement description, Structure summary