Research workbench
Structure of ALPHA6BETA1 integrin in complex with laminin-511
Analyse Structure of ALPHA6BETA1 integrin in complex with laminin-511 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7CEC
- Type
- protein
- Length
- 2,238 residues
- Chains
- 9
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Integrin alpha-6; Integrin beta-1; Laminin subunit alpha-5; Laminin subunit beta-1…
- UniProt
- P23229, P05556, O15230, P07942, P11047
- Ligands
- NAG, CA, MN
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · 9 distinct chains · 17% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Integrin alpha-6 | protein | 553 | 2% helix, 38% strand | P23229 |
| B | Integrin beta-1 | protein | 427 | 26% helix, 26% strand | P05556 |
| C | Laminin subunit alpha-5 | protein | 574 | 8% helix, 37% strand | O15230 |
| D | Laminin subunit beta-1 | protein | 47 | 94% helix, 0% strand | P07942 |
| E | Laminin subunit gamma-1 | protein | 44 | 66% helix, 2% strand | P11047 |
| F | TS2/16 VH(S112C)-SARAH,TS2/16 VH(S112C)-sarah | protein | 171 | 29% helix, 35% strand | — |
| G | TS2/16 vl-SARAH(S37C),TS2/16 vl-SARAH(S37C) | protein | 160 | 29% helix, 33% strand | — |
| H | Huts-4 VH(S112C)-SARAH,HUTS-4 VH(S112C)-sarah | protein | 122 | 2% helix, 43% strand | — |
| I | Huts-4 VL(C87Y)-SARAH(S37C),HUTS-4 VL(C87Y)-SARAH(S37C) | protein | 140 | 23% helix, 35% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains C, A, B, G
- CA · Calcium ion · metal · 4 copies · chains A, C
- MN · Manganese (II) ion · metal · 3 copies · chains B, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 692 | 0.85 | 0.89 | 96 | empty |
| 2 | 1017 | 0.78 | 0.80 | 82 | empty |
| 3 | 336 | 0.77 | 0.88 | 56 | empty |
| 4 | 487 | 0.75 | 0.84 | 61 | empty |
| 5 | 688 | 0.70 | 0.77 | 84 | empty |
Interfaces
16 interfaces between chains.
- F–G · 2678 Ų buried · 23 hydrogen bonds · protein-protein
- A–B · 1772 Ų buried · 13 hydrogen bonds · protein-protein
- H–I · 1260 Ų buried · 15 hydrogen bonds · protein-protein
- C–E · 989 Ų buried · 19 hydrogen bonds · protein-protein
- D–E · 906 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 24 disulfide, 7 glycan (disulfide, N-glycosylation).
Compared structures
- 7CEC · Structure of alpha6beta1 integrin in complex with laminin-511 · the same entry in another collection · chain I against I, 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 0.96
- P07942 · AlphaFold monomer V2.0 prediction for laminin subunit beta-1 (P07942) · a predicted model of the same protein · chain D against A, TM-score 0.87
- P11047 · AlphaFold monomer V2.0 prediction for laminin subunit gamma-1 (P11047) · a predicted model of the same protein · chain E against A, TM-score 0.72
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
- Every structure of UniProt O15230
- Every structure of UniProt P07942
- Every structure of UniProt P11047
- Elsewhere: RCSB PDB 7CEC · PDBe 7CEC · UniProt P23229 · UniProt P05556 · UniProt O15230 · UniProt P07942 · UniProt P11047
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