4NEH
An internal ligand-bound, metastable state of a leukocyte integrin, aXb2
- PDB DOI: https://doi.org/10.2210/pdb4NEH/pdb
- Classification: CELL ADHESION
- Organism(s): Homo sapiens
- Expression System: Homo sapiens
- Mutation(s): No
- Deposited: 2013-10-29 Released: 2014-01-15
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.75 Å
- R-Value Free: 0.225
- R-Value Work: 0.193
- R-Value Observed: 0.194
This is version 3.2 of the entry. See complete history.
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Integrin alpha-X | 1,094 | Homo sapiens | Mutation(s): 0 Gene Names: ITGAX, CD11C |  | |
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 | |||||
| |||||
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 2 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Integrin beta-2 | 686 | Homo sapiens | Mutation(s): 0 Gene Names: ITGB2, CD18, 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 | |||||
| |||||
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 | C, F, G, H | 2 |  | N-Glycosylation | |
Glycosylation Resources | |||||
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT | |||||
Entity ID: 4 | |||||
|---|---|---|---|---|---|
| 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 | D | 3 |  | N-Glycosylation | |
Glycosylation Resources | |||||
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE | |||||
Entity ID: 5 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
| alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[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 | E | 7 |  | N-Glycosylation | |
Glycosylation Resources | |||||
GlyTouCan: G07617FP GlyCosmos: G07617FP GlyGen: G07617FP | |||||
Small Molecules
| Ligands 5 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| NAG Query on NAG | M [auth A] | 2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N |  | ||
| CA Query on CA | I [auth A], K [auth A], L [auth A], P [auth B], Q [auth B] | CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N |  | ||
| CL Query on CL | N [auth A] | CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M |  | ||
| MG Query on MG | J [auth A], R [auth B] | MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N |  | ||
| NA Query on NA | O [auth A] | SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.75 Å
- R-Value Free: 0.225
- R-Value Work: 0.193
- R-Value Observed: 0.194
- Space Group: P 21 21 21
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 126.967 | α = 90 |
| b = 131.444 | β = 90 |
| c = 190.477 | γ = 90 |
| Software Name | Purpose |
|---|---|
| PHASER | phasing |
| PHENIX | refinement |
| XDS | data reduction |
| XDS | data scaling |
Entry History
Deposition Data
- Released Date: 2014-01-15 Deposition Author(s): Sen, M., Yuki, K., Springer, T.A.
Revision History (Full details and data files)
- Version 1.0: 2014-01-15
Type: Initial release - Version 2.0: 2020-06-03
Changes: Atomic model, Data collection, Database references, Derived calculations - Version 3.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary - Version 3.1: 2021-06-02
Changes: Source and taxonomy, Structure summary - Version 3.2: 2023-09-20
Changes: Data collection, Database references, Refinement description
