MolNFT v1 · #160766 · protein
Crystal structure of a dnan sliding clamp (DNA polymerase III subunit beta) from rickettsia rickettsii bound to griselimycin
6PTV · Beta sliding clamp: “Crystal structure of a dnan sliding clamp (DNA polymerase III subunit beta) from rickettsia rickettsii bound…”. X-ray diffraction, 1 ligand (ACE), 11 pockets (best druggability 0.66). MolNFT v1 #160766 on…
- PDB
- 6PTV
- Type
- protein
- Length
- 1,531 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta sliding clamp; ACE-mva-MP8-nzc-leu-MP8-leu-mva-pro-mlu-gly
- UniProt
- A0A0H3AWV3
- Ligands
- ACE
- Pockets
- 11 · best druggability 0.66
Structure
x-ray diffraction · 5 distinct chains · 22% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta sliding clamp | protein | 380 | 22% helix, 43% strand | A0A0H3AWV3 |
| B | Beta sliding clamp | protein | 376 | 22% helix, 43% strand | A0A0H3AWV3 |
| X, Y | ACE-mva-MP8-nzc-leu-MP8-leu-mva-pro-mlu-gly | protein | 10 | 0% helix, 0% strand | — |
| C | Beta sliding clamp | protein | 374 | 22% helix, 44% strand | A0A0H3AWV3 |
| D | Beta sliding clamp | protein | 381 | 24% helix, 43% strand | A0A0H3AWV3 |
Ligands and binding sites
- ACE · Acetyl group · ligand · 2 copies · chains B, X, C, Y
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 2 copies · chains A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 686 | 0.66 | 0.75 | 50 | empty |
| 2 | 105 | 0.51 | 0.82 | 15 | empty |
| 3 | 105 | 0.45 | 0.79 | 17 | empty |
| 4 | 92 | 0.41 | 0.78 | 17 | empty |
| 5 | 79 | 0.40 | 0.78 | 17 | MPD |
Interfaces
7 interfaces between chains.
- A–B · 1246 Ų buried · 22 hydrogen bonds · protein-protein
- C–D · 1245 Ų buried · 21 hydrogen bonds · protein-protein
- B–X · 513 Ų buried · 2 hydrogen bonds · protein-protein
- C–Y · 506 Ų buried · 2 hydrogen bonds · protein-protein
- B–D · 177 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 modified, 2 covalent (nonstandard, methylation, covalent ligand).
Compared structures
- 6PTV · Crystal structure of a DnaN sliding clamp (DNA polymerase III subunit beta) from… · 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 A0A0H3AWV3
- Elsewhere: RCSB PDB 6PTV · PDBe 6PTV · UniProt A0A0H3AWV3
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