Research workbench
Mutant DNA polymerase sliding clamp from mycobacterium tuberculosis with bound P7 peptide
Analyse Mutant DNA polymerase sliding clamp from mycobacterium tuberculosis with bound… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6FVO
- Type
- protein
- Length
- 1,553 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, CA
- Pockets
- 17 · best druggability 0.65
Structure
x-ray diffraction · 4 distinct chains · 22% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Beta sliding clamp | protein | 389 | 22% helix, 43% strand | P9WNU0 |
| B | Beta sliding clamp | protein | 376 | 22% helix, 45% strand | P9WNU0 |
| D | Beta sliding clamp | protein | 379 | 22% helix, 43% strand | P9WNU0 |
| H, I, J, K | P7 peptide | protein | 5 | 0% helix, 0% strand | — |
Ligands and binding sites
- ACE · Acetyl group · ligand · 4 copies · chains A, H, B, I, C, J, D, K
- CA · Calcium ion · metal · 4 copies · chains B, I, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 109 | 0.65 | 0.89 | 26 | empty |
| 2 | 638 | 0.64 | 0.75 | 56 | ACE |
| 3 | 153 | 0.63 | 0.85 | 35 | empty |
| 4 | 587 | 0.62 | 0.74 | 49 | empty |
| 5 | 63 | 0.58 | 0.89 | 29 | empty |
Interfaces
9 interfaces between chains.
- C–D · 1176 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 1149 Ų buried · 20 hydrogen bonds · protein-protein
- A–D · 668 Ų buried · 4 hydrogen bonds · protein-protein
- A–H · 561 Ų buried · 4 hydrogen bonds · protein-protein
- C–J · 546 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent, 4 modified (covalent ligand, nonstandard).
Compared structures
- 6FVO · Mutant DNA polymerase sliding clamp from Mycobacterium tuberculosis with bound P7 peptide · the same entry in another collection · chain K against K, TM-score 1.00
- P9WNU0 · AlphaFold monomer V2.0 prediction for beta sliding clamp (P9WNU0) · a predicted model of the same protein · chain D 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 6FVO · PDBe 6FVO · UniProt P9WNU0
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