MolNFT v1 · #184957 · protein
Short wilavidin apo form
7P8Y: “Short wilavidin apo form”. X-ray diffraction, 4 pockets (best druggability 0.59). MolNFT v1 #184957 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7P8Y
- Type
- protein
- Length
- 426 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Wilavidin
- UniProt
- A0A3A4VWA2
- Pockets
- 4 · best druggability 0.59
Structure
x-ray diffraction · 2 distinct chains · 3% helix, 65% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Wilavidin | protein | 107 | 3% helix, 65% strand | A0A3A4VWA2 |
| C, D | Wilavidin | protein | 106 | 3% helix, 64% strand | A0A3A4VWA2 |
Ligands and binding sites
- 1PE · Pentaethylene glycol · additive · 6 copies · chains A, B, C, D
- P6G · Hexaethylene glycol · additive · 4 copies · chains A, B, C
- PEG · Di(hydroxyethyl)ether · additive · chains A
- PGE · Triethylene glycol · additive · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 104 | 0.59 | 0.86 | 20 | 1PE |
| 2 | 103 | 0.57 | 0.85 | 19 | 1PE |
| 3 | 95 | 0.57 | 0.86 | 20 | 1PE |
| 4 | 95 | 0.57 | 0.86 | 19 | 1PE |
Interfaces
2 interfaces between chains.
- A–D · 1726 Ų buried · 16 hydrogen bonds · protein-protein
- B–C · 1715 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 7P8Y · Short wilavidin apo form · the same entry in another collection · chain A against A, TM-score 1.00
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 A0A3A4VWA2
- Elsewhere: RCSB PDB 7P8Y · PDBe 7P8Y · UniProt A0A3A4VWA2
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