Research workbench
An internal ligand-bound, metastable state of a leukocyte integrin, AXB2
Analyse An internal ligand-bound, metastable state of a leukocyte integrin, AXB2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4NEN
- Type
- protein
- Length
- 1,728 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Integrin alpha-X; Integrin beta-2
- UniProt
- P20702, P05107
- Ligands
- NAG, MAN, BMA, CA, MG, CL
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 14% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Integrin alpha-X | protein | 1063 | 10% helix, 45% strand | P20702 |
| B | Integrin beta-2 | protein | 665 | 20% helix, 28% strand | P05107 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 12 copies · chains A, B
- MAN · alpha-D-mannopyranose · sugar · 3 copies · chains A
- BMA · beta-D-mannopyranose · sugar · chains A
- CA · Calcium ion · metal · 5 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- CL · Chloride ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1099 | 0.82 | 0.83 | 95 | empty |
| 2 | 815 | 0.78 | 0.81 | 66 | empty |
| 3 | 580 | 0.71 | 0.79 | 54 | empty |
| 4 | 491 | 0.69 | 0.79 | 47 | empty |
| 5 | 473 | 0.65 | 0.78 | 63 | empty |
Interfaces
1 interface between chains.
- A–B · 3679 Ų buried · 34 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 37 disulfide, 6 glycan (disulfide, N-glycosylation).
Compared structures
- 4NEN · An internal ligand-bound, metastable state of a leukocyte integrin, aXb2 · the same entry in another collection · chain A against A, TM-score 1.00
- P20702 · AlphaFold monomer V2.0 prediction for integrin alpha-X (P20702) · a predicted model of the same protein · chain A against A, TM-score 0.93
- P05107 · AlphaFold monomer V2.0 prediction for integrin beta-2 (P05107) · a predicted model of the same protein · chain B against A, TM-score 0.91
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P20702
- Every structure of UniProt P05107
- Elsewhere: RCSB PDB 4NEN · PDBe 4NEN · UniProt P20702 · UniProt P05107
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