MolNFT v1 · #101723 · protein
ALPHAVBETA3 integrin in complex with monoclonal antibody Fab fragment.
4O02 · Integrin alpha-V: “ALPHAVBETA3 integrin in complex with monoclonal antibody Fab fragment.”. X-ray diffraction, 5 ligands (NAG, MAN, BMA), 20 pockets (best druggability 0.84). MolNFT v1 #101723 on GenesisL1: 3D structure, binding…
- PDB
- 4O02
- Type
- protein
- Length
- 2,034 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Integrin alpha-V; Integrin beta-3; 17E6 light chain; 17E6 heavy chain
- UniProt
- P06756, P05106
- Ligands
- NAG, MAN, BMA, MN, NO3
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 4 distinct chains · 8% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Integrin alpha-V | protein | 915 | 4% helix, 41% strand | P06756 |
| B | Integrin beta-3 | protein | 687 | 16% helix, 27% strand | P05106 |
| L | 17E6 light chain | protein | 214 | 6% helix, 47% strand | — |
| H | 17E6 heavy chain | protein | 218 | 6% helix, 44% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 17 copies · chains A, B
- MAN · alpha-D-mannopyranose · sugar · 8 copies · chains A
- BMA · beta-D-mannopyranose · sugar · 5 copies · chains A
- MN · Manganese (II) ion · metal · 5 copies · chains A, B
- NO3 · Nitrate ion · ion · 2 copies · chains A, L, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 954 | 0.84 | 0.86 | 136 | empty |
| 2 | 763 | 0.81 | 0.85 | 87 | empty |
| 3 | 945 | 0.81 | 0.83 | 123 | empty |
| 4 | 578 | 0.80 | 0.86 | 52 | empty |
| 5 | 1042 | 0.72 | 0.75 | 82 | empty |
Interfaces
4 interfaces between chains.
- A–B · 2213 Ų buried · 13 hydrogen bonds · protein-protein
- L–H · 1604 Ų buried · 10 hydrogen bonds · protein-protein
- A–H · 840 Ų buried · 16 hydrogen bonds · protein-protein
- A–L · 196 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 36 disulfide, 10 glycan (disulfide, N-glycosylation).
Compared structures
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 4O02 · PDBe 4O02 · UniProt P06756 · UniProt P05106
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