MolNFT v1 · #146586 · protein
Crystal structure of DNA polymerase III subunit beta from mycobacterium marinum in complex with a natural product
6DLY · Beta sliding clamp: “Crystal structure of DNA polymerase III subunit beta from mycobacterium marinum in complex with a natural…”. X-ray diffraction, 1 ligand (ACE), 4 pockets (best druggability 0.64). MolNFT v1 #146586 on GenesisL1…
- PDB
- 6DLY
- Type
- protein
- Length
- 779 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta sliding clamp; Natural product peptide
- UniProt
- B2HI47
- Ligands
- ACE
- Pockets
- 4 · best druggability 0.64
Structure
x-ray diffraction · 3 distinct chains · 22% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta sliding clamp | protein | 375 | 23% helix, 43% strand | B2HI47 |
| B | Beta sliding clamp | protein | 384 | 22% helix, 43% strand | B2HI47 |
| C, D | Natural product peptide | protein | 10 | 0% helix, 0% strand | — |
Ligands and binding sites
- ACE · Acetyl group · ligand · 2 copies · chains A, C, B, D
- EDO · 1,2-ethanediol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 213 | 0.64 | 0.83 | 30 | empty |
| 2 | 119 | 0.57 | 0.84 | 27 | empty |
| 3 | 58 | 0.35 | 0.78 | 15 | empty |
| 4 | 67 | 0.31 | 0.74 | 16 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1033 Ų buried · 20 hydrogen bonds · protein-protein
- A–C · 632 Ų buried · 3 hydrogen bonds · protein-protein
- B–D · 619 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 12 modified, 2 covalent (nonstandard, methylation, covalent ligand).
Compared structures
- 6DLY · Crystal structure of DNA polymerase III subunit beta from Mycobacterium marinum in… · the same entry in another collection · chain B against B, 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 B2HI47
- Elsewhere: RCSB PDB 6DLY · PDBe 6DLY · UniProt B2HI47
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