Research workbench
Mutant DNA polymerase sliding clamp from escherichia COLI with bound P7 peptide
Analyse Mutant DNA polymerase sliding clamp from escherichia COLI with bound P7 peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6FVM
- Type
- protein
- Length
- 746 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta sliding clamp; P7 peptide
- UniProt
- P0A990
- Ligands
- ACE, CA
- Pockets
- 11 · best druggability 0.41
Structure
x-ray diffraction · 2 distinct chains · 22% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Beta sliding clamp | protein | 368 | 22% helix, 47% strand | P0A990 |
| H, I | P7 peptide | protein | 5 | 0% helix, 0% strand | — |
Ligands and binding sites
- ACE · Acetyl group · ligand · 2 copies · chains A, H, B, I
- CA · Calcium ion · metal · chains A
- 1PE · Pentaethylene glycol · additive · 9 copies · chains A, B
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 87 | 0.41 | 0.78 | 17 | empty |
| 2 | 68 | 0.36 | 0.77 | 14 | empty |
| 3 | 56 | 0.35 | 0.79 | 15 | empty |
| 4 | 61 | 0.34 | 0.77 | 19 | empty |
| 5 | 89 | 0.34 | 0.74 | 22 | 1PE |
Interfaces
3 interfaces between chains.
- A–B · 1307 Ų buried · 31 hydrogen bonds · protein-protein
- A–H · 549 Ų buried · 5 hydrogen bonds · protein-protein
- B–I · 547 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent, 2 modified (covalent ligand, nonstandard).
Compared structures
- 6FVM · Mutant DNA polymerase sliding clamp from Escherichia coli with bound P7 peptide · the same entry in another collection · chain A against A, TM-score 1.00
- P0A990 · AlphaFold monomer V2.0 prediction for beta sliding clamp (P0A990) · a predicted model of the same protein · chain B 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 P0A990
- Elsewhere: RCSB PDB 6FVM · PDBe 6FVM · UniProt P0A990
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