MolNFT v1 · #7070 · protein
Crystal structure of botrocetin
1FVU · Botrocetin alpha chain: “Crystal structure of botrocetin”. X-ray diffraction, 1 ligand (MG), 2 pockets (best druggability 0.85). MolNFT v1 #7070 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1FVU
- Type
- protein
- Length
- 508 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Botrocetin alpha chain; Botrocetin beta chain
- UniProt
- P22029, P22030
- Ligands
- MG
- Pockets
- 2 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 18% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Botrocetin alpha chain | protein | 133 | 20% helix, 32% strand | P22029 |
| B, D | Botrocetin beta chain | protein | 121 | 16% helix, 32% strand | P22030 |
Ligands and binding sites
- MG · Magnesium ion · metal · 2 copies · chains B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 962 | 0.85 | 0.86 | 86 | empty |
| 2 | 227 | 0.60 | 0.80 | 28 | empty |
Interfaces
6 interfaces between chains.
- C–D · 1746 Ų buried · 22 hydrogen bonds · protein-protein
- A–B · 1731 Ų buried · 26 hydrogen bonds · protein-protein
- B–D · 510 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 365 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 343 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 disulfide (disulfide).
Compared structures
- 1FVU · Crystal structure of botrocetin · the same entry in another collection · chain A against A, TM-score 1.00
- P22029 · AlphaFold monomer V2.0 prediction for snaclec botrocetin subunit alpha (P22029) · a predicted model of the same protein · chain A against A, TM-score 0.96
- P22030 · AlphaFold monomer V2.0 prediction for snaclec botrocetin subunit beta (P22030) · a predicted model of the same protein · chain B against A, TM-score 0.90
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 P22029
- Every structure of UniProt P22030
- Elsewhere: RCSB PDB 1FVU · PDBe 1FVU · UniProt P22029 · UniProt P22030
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