MolNFT v1 · #183434 · protein + DNA
Vibrio cholerae PARA2-atpys-DNA filament
7NPF · Aaa family ATPase: “Vibrio cholerae PARA2-atpys-DNA filament”. Electron microscopy, 2 ligands (AGS, MG), 20 pockets (best druggability 0.85). MolNFT v1 #183434 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7NPF
- Type
- protein + DNA
- Length
- 3,322 residues
- Chains
- 10
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Aaa family ATPase; DNA (49-mer)
- UniProt
- A0A085S0Z4
- Ligands
- AGS, MG
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · 4 distinct chains · 48% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, G | Aaa family ATPase | protein | 404 | 47% helix, 9% strand | A0A085S0Z4 |
| B, D, F, H | Aaa family ATPase | protein | 402 | 48% helix, 7% strand | A0A085S0Z4 |
| I | DNA (49-mer) | dna | 49 | — | — |
| J | DNA (49-mer) | dna | 49 | — | — |
Ligands and binding sites
- AGS · Phosphothiophosphoric acid-adenylate ester · ligand · 8 copies · chains A, B, C, D, E, F, G, H
- MG · Magnesium ion · metal · 8 copies · chains A, B, C, D, E, F, G, H
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 | 1147 | 0.85 | 0.86 | 135 | empty |
| 2 | 1045 | 0.85 | 0.86 | 104 | MG, AGS |
| 3 | 988 | 0.85 | 0.86 | 106 | MG, AGS |
| 4 | 994 | 0.85 | 0.86 | 114 | empty |
| 5 | 1173 | 0.85 | 0.86 | 135 | empty |
Interfaces
29 interfaces between chains.
- G–H · 2954 Ų buried · 20 hydrogen bonds · protein-protein
- A–B · 2953 Ų buried · 20 hydrogen bonds · protein-protein
- E–F · 2952 Ų buried · 20 hydrogen bonds · protein-protein
- C–D · 2952 Ų buried · 20 hydrogen bonds · protein-protein
- I–J · 2153 Ų buried · 159 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 8 covalent (covalent ligand).
Compared structures
- 7NPF · Vibrio cholerae ParA2-ATPyS-DNA filament · the same entry in another collection · chain A against A, TM-score 1.00
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 A0A085S0Z4
- Elsewhere: RCSB PDB 7NPF · PDBe 7NPF · UniProt A0A085S0Z4
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