MolNFT v1 · #81711 · protein
2.7 ångström crystal structure of BONT/AI in complex with ntnha
3V0A: “2.7 ångström crystal structure of BONT/AI in complex with ntnha”. X-ray diffraction, 3 ligands (ZN, CA, SO4), 20 pockets (best druggability 0.87). MolNFT v1 #81711 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3V0A
- Type
- protein
- Length
- 2,549 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- BONT/A; Ntnh; Llama antibody F12
- UniProt
- Q7B8V4, Q45914
- Ligands
- ZN, CA, SO4
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 3 distinct chains · 30% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | BONT/A | protein | 1280 | 30% helix, 24% strand | Q7B8V4 |
| B | Ntnh | protein | 1150 | 33% helix, 25% strand | Q45914 |
| C | Llama antibody F12 | protein | 119 | 5% helix, 45% strand | — |
Ligands and binding sites
- ZN · Zinc ion · metal · chains A
- CA · Calcium ion · metal · chains A
- SO4 · Sulfate ion · ion · 20 copies · chains A, B, C
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · 4 copies · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1015 | 0.87 | 0.88 | 103 | empty |
| 2 | 1027 | 0.82 | 0.83 | 95 | SO4 |
| 3 | 626 | 0.79 | 0.84 | 64 | SO4 |
| 4 | 716 | 0.78 | 0.82 | 87 | empty |
| 5 | 391 | 0.77 | 0.87 | 43 | empty |
Interfaces
2 interfaces between chains.
- A–B · 3998 Ų buried · 44 hydrogen bonds · protein-protein
- A–C · 713 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 3V0A · 2.7 angstrom crystal structure of BoNT/Ai in complex with NTNHA · the same entry in another collection · chain A against A, TM-score 1.00
- Q45914 · AlphaFold monomer V2.0 prediction for non-toxic nonhemagglutinin type a (Q45914) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 Q7B8V4
- Every structure of UniProt Q45914
- Elsewhere: RCSB PDB 3V0A · PDBe 3V0A · UniProt Q7B8V4 · UniProt Q45914
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.