MolNFT v1 · #181600 · protein
LC/A-jpu-B9-jpu-A11-jpu-G11
7LZP · Botulinum neurotoxin a light chain: “LC/A-jpu-B9-jpu-A11-jpu-G11”. X-ray diffraction, 1 ligand (ZN), 16 pockets (best druggability 0.82). MolNFT v1 #181600 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7LZP
- Type
- protein
- Length
- 1,541 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Botulinum neurotoxin a light chain; Jpu-G11; Jpu-A11; Jpu-B9
- EC
- 3.4.24.69
- UniProt
- P0DPI0
- Ligands
- ZN
- Pockets
- 16 · best druggability 0.82
Structure
x-ray diffraction · 8 distinct chains · 18% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Botulinum neurotoxin a light chain (EC 3.4.24.69) | protein | 419 | 31% helix, 21% strand | P0DPI0 |
| C | Jpu-G11 | protein | 116 | 3% helix, 52% strand | — |
| D | Botulinum neurotoxin a light chain (EC 3.4.24.69) | protein | 421 | 31% helix, 19% strand | P0DPI0 |
| E | Jpu-A11 | protein | 128 | 2% helix, 47% strand | — |
| G | Jpu-B9 | protein | 110 | 3% helix, 50% strand | — |
| F | Jpu-G11 | protein | 112 | 0% helix, 52% strand | — |
| B | Jpu-A11 | protein | 129 | 2% helix, 47% strand | — |
| H | Jpu-B9 | protein | 106 | 3% helix, 52% strand | — |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 705 | 0.82 | 0.86 | 77 | ZN |
| 2 | 454 | 0.73 | 0.83 | 43 | empty |
| 3 | 464 | 0.72 | 0.82 | 41 | ZN |
| 4 | 276 | 0.69 | 0.84 | 38 | empty |
| 5 | 56 | 0.67 | 0.96 | 17 | empty |
Interfaces
9 interfaces between chains.
- A–D · 1864 Ų buried · 26 hydrogen bonds · protein-protein
- A–B · 1192 Ų buried · 16 hydrogen bonds · protein-protein
- D–E · 1088 Ų buried · 14 hydrogen bonds · protein-protein
- D–H · 988 Ų buried · 16 hydrogen bonds · protein-protein
- A–G · 973 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
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 7LZP · PDBe 7LZP · UniProt P0DPI0
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