Research workbench
Crystal structure of LC/A-jpu-C10-jpu-D12-jpu-B8-jpu-G3-cia-F12-cia- D12
Analyse Crystal structure of LC/A-jpu-C10-jpu-D12-jpu-B8-jpu-G3-cia-F12-cia- D12 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7M1H
- Type
- protein
- Length
- 1,141 residues
- Chains
- 7
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Botulinum neurotoxin a light chain; Jpu-D12; Cia-F12; Cia-D12; Jpu-G3; Jpu-C10; Jpu-B8
- EC
- 3.4.24.69
- UniProt
- P0DPI0
- Ligands
- ZN
- Pockets
- 11 · best druggability 0.83
Structure
x-ray diffraction · 7 distinct chains · 16% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Botulinum neurotoxin a light chain (EC 3.4.24.69) | protein | 430 | 34% helix, 17% strand | P0DPI0 |
| B | Jpu-D12 | protein | 123 | 5% helix, 50% strand | — |
| C | Cia-F12 | protein | 117 | 5% helix, 48% strand | — |
| D | Cia-D12 | protein | 123 | 7% helix, 49% strand | — |
| E | Jpu-G3 | protein | 123 | 5% helix, 48% strand | — |
| F | Jpu-C10 | protein | 121 | 2% helix, 54% strand | — |
| G | Jpu-B8 | protein | 104 | 3% helix, 56% strand | — |
Ligands and binding sites
- ZN · Zinc ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1153 | 0.83 | 0.84 | 119 | empty |
| 2 | 501 | 0.66 | 0.77 | 48 | empty |
| 3 | 394 | 0.61 | 0.77 | 47 | empty |
| 4 | 138 | 0.58 | 0.83 | 26 | empty |
| 5 | 58 | 0.58 | 0.90 | 23 | empty |
Interfaces
8 interfaces between chains.
- A–F · 1260 Ų buried · 17 hydrogen bonds · protein-protein
- A–E · 1071 Ų buried · 19 hydrogen bonds · protein-protein
- A–G · 812 Ų buried · 7 hydrogen bonds · protein-protein
- A–D · 789 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 740 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide (disulfide).
Compared structures
- 7M1H · Crystal structure of LC/A-JPU-C10-JPU-D12-JPU-B8-JPU-G3-ciA-F12-ciA-D12 · the same entry in another collection · chain G against G, TM-score 1.00
- P0DPI0 · AlphaFold monomer V2.0 prediction for botulinum neurotoxin type a (P0DPI0) · a predicted model of the same protein · chain A against A, TM-score 0.94
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 P0DPI0
- Elsewhere: RCSB PDB 7M1H · PDBe 7M1H · UniProt P0DPI0
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