MolNFT v1 · #149276 · protein
DNA polymerase sliding clamp from mycobacterium tuberculosis with bound P7 peptide
6FVN · Beta sliding clamp: “DNA polymerase sliding clamp from mycobacterium tuberculosis with bound P7 peptide”. X-ray diffraction, 1 ligand (ACE), 14 pockets (best druggability 0.71). MolNFT v1 #149276 on GenesisL1: 3D structure, binding…
- PDB
- 6FVN
- Type
- protein
- Length
- 1,523 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta sliding clamp; P7 peptide
- UniProt
- P9WNU0
- Ligands
- ACE
- Pockets
- 14 · best druggability 0.71
Structure
x-ray diffraction · 5 distinct chains · 20% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta sliding clamp | protein | 379 | 19% helix, 42% strand | P9WNU0 |
| J, K, H, I | P7 peptide | protein | 5 | 0% helix, 0% strand | — |
| B | Beta sliding clamp | protein | 372 | 20% helix, 44% strand | P9WNU0 |
| C | Beta sliding clamp | protein | 372 | 20% helix, 42% strand | P9WNU0 |
| D | Beta sliding clamp | protein | 380 | 21% helix, 41% strand | P9WNU0 |
Ligands and binding sites
- ACE · Acetyl group · ligand · 4 copies · chains A, J, D, B, K, C, H, I
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 92 | 0.71 | 0.94 | 32 | empty |
| 2 | 743 | 0.71 | 0.77 | 89 | empty |
| 3 | 295 | 0.52 | 0.74 | 39 | empty |
| 4 | 149 | 0.50 | 0.79 | 29 | empty |
| 5 | 83 | 0.46 | 0.81 | 23 | empty |
Interfaces
9 interfaces between chains.
- C–D · 1190 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 1125 Ų buried · 18 hydrogen bonds · protein-protein
- A–D · 618 Ų buried · 1 hydrogen bond · protein-protein
- A–J · 506 Ų buried · 4 hydrogen bonds · protein-protein
- D–I · 506 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent, 4 modified (covalent ligand, nonstandard).
Compared structures
- 6FVN · DNA polymerase sliding clamp from Mycobacterium tuberculosis with bound P7 peptide · the same entry in another collection · chain I against I, TM-score 1.00
- P9WNU0 · AlphaFold monomer V2.0 prediction for beta sliding clamp (P9WNU0) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 P9WNU0
- Elsewhere: RCSB PDB 6FVN · PDBe 6FVN · UniProt P9WNU0
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