Research workbench
The therapeutic antibody LM609 selectively inhibits ligand binding to human alpha-V beta-3 integrin via steric hindrance
Analyse The therapeutic antibody LM609 selectively inhibits ligand binding to human… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6AVQ
- Type
- protein
- Length
- 2,040 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Integrin alpha-V; Integrin beta-3; LM609 Fab heavy chain; LM609 Fab light chain
- UniProt
- P06756, P05106
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · 4 distinct chains · 10% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Integrin alpha-V | protein | 927 | 3% helix, 45% strand | P06756 |
| B | Integrin beta-3 | protein | 688 | 21% helix, 30% strand | P05106 |
| H | LM609 Fab heavy chain | protein | 214 | 7% helix, 54% strand | — |
| L | LM609 Fab 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 | 1030 | 0.86 | 0.87 | 174 | empty |
| 2 | 822 | 0.84 | 0.86 | 112 | empty |
| 3 | 733 | 0.83 | 0.87 | 105 | empty |
| 4 | 751 | 0.83 | 0.87 | 121 | empty |
| 5 | 925 | 0.82 | 0.84 | 139 | empty |
Interfaces
6 interfaces between chains.
- A–B · 1008 Ų buried · 3 hydrogen bonds · protein-protein
- H–L · 645 Ų buried · 0 hydrogen bonds · protein-protein
- A–L · 174 Ų buried · 2 hydrogen bonds · protein-protein
- B–L · 151 Ų buried · 0 hydrogen bonds · protein-protein
- B–H · 138 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6AVQ · The Therapeutic Antibody LM609 Selectively Inhibits Ligand Binding to Human alpha-V… · 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 0.98
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 6AVQ · PDBe 6AVQ · UniProt P06756 · UniProt P05106
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