MolNFT v1 · #114478 · protein
Crystal structure of SXN101959, a clostridium botulinum neurotoxin type D derivative and targeted secretion inhibitor
5BQM: “Crystal structure of SXN101959, a clostridium botulinum neurotoxin type D derivative and targeted secretion…”. X-ray diffraction, 1 ligand (ZN), 20 pockets (best druggability 0.85). MolNFT v1 #114478 on GenesisL1: 3D structure…
- PDB
- 5BQM
- Type
- protein
- Length
- 1,660 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Botulinum neurotoxin type D; SOMATOLIBERIN,BOTULINUM neurotoxin type D
- EC
- 3.4.24.69
- UniProt
- P19321, P01286
- Ligands
- ZN
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 4 distinct chains · 39% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Botulinum neurotoxin type D (EC 3.4.24.69) | protein | 442 | 30% helix, 19% strand | P19321 |
| B | SOMATOLIBERIN,BOTULINUM neurotoxin type D (EC 3.4.24.69) | protein | 387 | 52% helix, 7% strand | P19321, P01286 |
| C | Botulinum neurotoxin type D (EC 3.4.24.69) | protein | 443 | 28% helix, 18% strand | P19321 |
| D | SOMATOLIBERIN,BOTULINUM neurotoxin type D (EC 3.4.24.69) | protein | 388 | 49% helix, 8% strand | P19321, P01286 |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 953 | 0.85 | 0.86 | 103 | empty |
| 2 | 116 | 0.79 | 0.98 | 25 | empty |
| 3 | 96 | 0.78 | 0.98 | 23 | empty |
| 4 | 287 | 0.73 | 0.86 | 50 | empty |
| 5 | 483 | 0.72 | 0.81 | 52 | empty |
Interfaces
6 interfaces between chains.
- A–B · 4970 Ų buried · 61 hydrogen bonds · protein-protein
- C–D · 4930 Ų buried · 65 hydrogen bonds · protein-protein
- B–D · 588 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 381 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 365 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 5BQM · Crystal structure of SXN101959, a Clostridium botulinum neurotoxin type D derivative and… · the same entry in another collection · chain A against A, TM-score 1.00
- P01286 · AlphaFold monomer V2.0 prediction for somatoliberin (P01286) · a predicted model of the same protein · chain B against A, TM-score 0.16
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 P19321
- Every structure of UniProt P01286
- Elsewhere: RCSB PDB 5BQM · PDBe 5BQM · UniProt P19321 · UniProt P01286
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