MolNFT v1 · #143309 · protein
Human alpha-V beta-3 integrin (intermediate conformation) in complex with the therapeutic antibody LM609
6AVR · Integrin alpha-V: “Human alpha-V beta-3 integrin (intermediate conformation) in complex with the therapeutic antibody LM609”. Electron microscopy, 20 pockets (best druggability 0.86). MolNFT v1 #143309 on GenesisL1: 3D structure…
- PDB
- 6AVR
- Type
- protein
- Length
- 2,034 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 0.86
Structure
electron microscopy · 4 distinct chains · 10% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Integrin alpha-V | protein | 924 | 3% helix, 45% strand | P06756 |
| B | Integrin beta-3 | protein | 685 | 21% helix, 29% 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 | 1002 | 0.86 | 0.87 | 166 | empty |
| 2 | 1109 | 0.84 | 0.85 | 123 | empty |
| 3 | 1118 | 0.83 | 0.84 | 184 | empty |
| 4 | 705 | 0.83 | 0.87 | 99 | empty |
| 5 | 1064 | 0.82 | 0.84 | 143 | empty |
Interfaces
6 interfaces between chains.
- A–B · 1106 Ų buried · 1 hydrogen bond · protein-protein
- H–L · 641 Ų buried · 0 hydrogen bonds · protein-protein
- A–L · 176 Ų buried · 2 hydrogen bonds · protein-protein
- B–L · 147 Ų buried · 0 hydrogen bonds · protein-protein
- B–H · 138 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6AVR · Human alpha-V beta-3 Integrin (intermediate 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 0.68
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 6AVR · PDBe 6AVR · UniProt P06756 · UniProt P05106
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