MolNFT v1 · #184958 · protein
Short wilavidin biotin complex
7P8Z: “Short wilavidin biotin complex”. X-ray diffraction, 2 ligands (BTN, NA), 6 pockets (best druggability 0.64). MolNFT v1 #184958 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7P8Z
- Type
- protein
- Length
- 428 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Wilavidin
- UniProt
- A0A3A4VWA2
- Ligands
- BTN, NA
- Pockets
- 6 · best druggability 0.64
Structure
x-ray diffraction · 1 distinct chain · 3% helix, 65% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Wilavidin | protein | 107 | 3% helix, 65% strand | A0A3A4VWA2 |
Ligands and binding sites
- BTN · Biotin · ligand · 4 copies · chains A, B, C, D
- NA · Sodium ion · metal · 2 copies · chains C, D
- EDO · 1,2-ethanediol · additive · 2 copies · chains B, C, D
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains B, D
- P33 · 3,6,9,12,15,18-hexaoxaicosane-1,20-diol · additive · 2 copies · chains C, D
- PG4 · Tetraethylene glycol · additive · chains A
- PGE · Triethylene glycol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 161 | 0.64 | 0.85 | 29 | EDO |
| 2 | 88 | 0.59 | 0.87 | 20 | BTN |
| 3 | 87 | 0.58 | 0.87 | 20 | BTN |
| 4 | 98 | 0.58 | 0.86 | 19 | BTN |
| 5 | 88 | 0.55 | 0.85 | 21 | BTN |
Interfaces
5 interfaces between chains.
- B–D · 1729 Ų buried · 17 hydrogen bonds · protein-protein
- A–C · 1728 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 395 Ų buried · 2 hydrogen bonds · protein-protein
- A–D · 69 Ų buried · 0 hydrogen bonds · protein-protein
- B–C · 65 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 7P8Z · Short wilavidin biotin complex · 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 7P8Z · PDBe 7P8Z · UniProt A0A3A4VWA2
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