Research workbench
Structure of integrin ALPHAXBETA2 ectodomain
Analyse Structure of integrin ALPHAXBETA2 ectodomain in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3K6S
- Type
- protein
- Length
- 6,432 residues
- Chains
- 8
- 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, CA, MG
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 4 distinct chains · 6% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Integrin alpha-X | protein | 1082 | 7% helix, 34% strand | P20702 |
| B, D, F, H | Integrin beta-2 | protein | 674 | 15% helix, 20% strand | P05107 |
| C, G | Integrin alpha-X | protein | 885 | 2% helix, 38% strand | P20702 |
| E | Integrin alpha-X | protein | 884 | 2% helix, 37% strand | P20702 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 36 copies · chains A, B, C, D, E, F, G, H
- MAN · alpha-D-mannopyranose · sugar · 6 copies · chains A, E, G
- CA · Calcium ion · metal · 16 copies · chains A, B, C, D, E, F, G, H
- MG · Magnesium ion · metal · 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, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 992 | 0.87 | 0.88 | 98 | empty |
| 2 | 1014 | 0.86 | 0.87 | 99 | empty |
| 3 | 919 | 0.86 | 0.87 | 86 | empty |
| 4 | 926 | 0.85 | 0.87 | 88 | empty |
| 5 | 1001 | 0.79 | 0.81 | 88 | empty |
Interfaces
10 interfaces between chains.
- A–B · 3729 Ų buried · 32 hydrogen bonds · protein-protein
- C–D · 3668 Ų buried · 30 hydrogen bonds · protein-protein
- G–H · 3410 Ų buried · 25 hydrogen bonds · protein-protein
- E–F · 3404 Ų buried · 27 hydrogen bonds · protein-protein
- A–C · 2469 Ų buried · 35 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 152 disulfide, 24 glycan (disulfide, N-glycosylation).
Compared structures
- 3K6S · Structure of integrin alphaXbeta2 ectodomain · the same entry in another collection · chain H against H, TM-score 1.00
- P05107 · AlphaFold monomer V2.0 prediction for integrin beta-2 (P05107) · a predicted model of the same protein · chain B against A, TM-score 0.94
- P20702 · AlphaFold monomer V2.0 prediction for integrin alpha-X (P20702) · a predicted model of the same protein · chain E against A, TM-score 0.93
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 3K6S · PDBe 3K6S · UniProt P20702 · UniProt P05107
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