Research workbench
Human alpha-V beta-3 integrin (open conformation) in complex with the therapeutic antibody LM609
Analyse Human alpha-V beta-3 integrin (open conformation) in complex with the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6AVU
- Type
- protein
- Length
- 1,809 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Integrin alpha-V; Integrin beta-3; Fab LM609 heavy chain; Fab LM609 light chain
- UniProt
- P06756, P05106
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · 4 distinct chains · 9% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Integrin alpha-V | protein | 923 | 3% helix, 46% strand | P06756 |
| B | Integrin beta-3 | protein | 461 | 23% helix, 30% strand | P05106 |
| H | Fab LM609 heavy chain | protein | 214 | 7% helix, 54% strand | — |
| L | Fab LM609 light chain | protein | 211 | 6% helix, 52% strand | — |
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 | 874 | 0.85 | 0.87 | 154 | empty |
| 2 | 780 | 0.84 | 0.87 | 107 | empty |
| 3 | 578 | 0.83 | 0.89 | 89 | empty |
| 4 | 1109 | 0.82 | 0.84 | 158 | empty |
| 5 | 695 | 0.81 | 0.86 | 112 | empty |
Interfaces
6 interfaces between chains.
- H–L · 647 Ų buried · 0 hydrogen bonds · protein-protein
- A–B · 340 Ų buried · 0 hydrogen bonds · protein-protein
- A–L · 174 Ų buried · 2 hydrogen bonds · protein-protein
- B–L · 149 Ų buried · 0 hydrogen bonds · protein-protein
- B–H · 135 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6AVU · Human alpha-V beta-3 Integrin (open conformation) in complex with the therapeutic… · the same entry in another collection · chain A against A, TM-score 1.00
- P06756 · AlphaFold monomer V2.0 prediction for integrin alpha-V (P06756) · a predicted model of the same protein · chain A against A, TM-score 0.63
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 P06756
- Every structure of UniProt P05106
- Elsewhere: RCSB PDB 6AVU · PDBe 6AVU · UniProt P06756 · UniProt P05106
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