MolNFT v1 · #175043 · protein
Crystal structure of ALPHA6BETA1 integrin headpiece
7CEB · Integrin alpha-6: “Crystal structure of ALPHA6BETA1 integrin headpiece”. X-ray diffraction, 3 ligands (NAG, CA, MG), 11 pockets (best druggability 0.78). MolNFT v1 #175043 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 7CEB
- Type
- protein
- Length
- 1,220 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Integrin alpha-6; Integrin beta-1; TS2/16 VH(S112C)-sarah; TS2/16 vl-SARAH(S37C)
- UniProt
- P23229, P05556
- Ligands
- NAG, CA, MG
- Pockets
- 11 · best druggability 0.78
Structure
x-ray diffraction · 4 distinct chains · 14% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Integrin alpha-6 | protein | 553 | 1% helix, 44% strand | P23229 |
| B | Integrin beta-1 | protein | 374 | 23% helix, 32% strand | P05556 |
| C | TS2/16 VH(S112C)-sarah | protein | 147 | 24% helix, 43% strand | — |
| D | TS2/16 vl-SARAH(S37C) | protein | 146 | 26% helix, 36% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains A, B, D
- CA · Calcium ion · metal · 4 copies · chains A, B
- MG · Magnesium ion · metal · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 509 | 0.78 | 0.85 | 53 | empty |
| 2 | 523 | 0.70 | 0.79 | 60 | empty |
| 3 | 505 | 0.65 | 0.77 | 65 | empty |
| 4 | 177 | 0.46 | 0.76 | 34 | empty |
| 5 | 141 | 0.43 | 0.75 | 27 | empty |
Interfaces
4 interfaces between chains.
- C–D · 2142 Ų buried · 22 hydrogen bonds · protein-protein
- A–B · 1735 Ų buried · 12 hydrogen bonds · protein-protein
- B–D · 575 Ų buried · 15 hydrogen bonds · protein-protein
- B–C · 406 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide, 6 glycan (disulfide, N-glycosylation).
Compared structures
- 7CEB · Crystal structure of alpha6beta1 integrin headpiece · the same entry in another collection · chain A against A, TM-score 1.00
- P23229 · AlphaFold monomer V2.0 prediction for integrin alpha-6 (P23229) · a predicted model of the same protein · chain A against A, TM-score 0.95
- P05556 · AlphaFold monomer V2.0 prediction for integrin beta-1 (P05556) · a predicted model of the same protein · chain B against A, TM-score 0.95
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 P23229
- Every structure of UniProt P05556
- Elsewhere: RCSB PDB 7CEB · PDBe 7CEB · UniProt P23229 · UniProt P05556
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