MolNFT v1 · #113494 · protein
The sliding clamp of mycobacterium smegmatis in complex with a natural product.
5AH4 · DNA polymerase III subunit beta: “The sliding clamp of mycobacterium smegmatis in complex with a natural product.”. X-ray diffraction, 2 ligands (ACE, NA), 5 pockets (best druggability 0.66). MolNFT v1 #113494 on GenesisL1: 3D…
- PDB
- 5AH4
- Type
- protein
- Length
- 780 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase III subunit beta; Cyclohexyl griselimycin
- EC
- 2.7.7.7
- UniProt
- A0QND6
- Ligands
- ACE, NA
- Pockets
- 5 · best druggability 0.66
Structure
x-ray diffraction · 3 distinct chains · 21% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase III subunit beta (EC 2.7.7.7) | protein | 380 | 21% helix, 43% strand | A0QND6 |
| B | DNA polymerase III subunit beta (EC 2.7.7.7) | protein | 380 | 21% helix, 43% strand | A0QND6 |
| C, D | Cyclohexyl griselimycin | protein | 10 | 0% helix, 10% strand | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 88 | 0.66 | 0.91 | 28 | empty |
| 2 | 283 | 0.61 | 0.79 | 45 | empty |
| 3 | 78 | 0.41 | 0.79 | 22 | empty |
| 4 | 144 | 0.40 | 0.74 | 30 | empty |
| 5 | 60 | 0.33 | 0.76 | 16 | empty |
Interfaces
6 interfaces between chains.
- B–D · 737 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 708 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 230 Ų buried · 0 hydrogen bonds · protein-protein
- C–D · 113 Ų buried · 0 hydrogen bonds · protein-protein
- B–C · 90 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 modified, 2 covalent (nonstandard, methylation, covalent ligand).
Compared structures
- 5AH4 · The sliding clamp of Mycobacterium smegmatis in complex with a natural product. · the same entry in another collection · chain A against A, TM-score 1.00
- A0QND6 · AlphaFold monomer V2.0 prediction for beta sliding clamp (A0QND6) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 A0QND6
- Elsewhere: RCSB PDB 5AH4 · PDBe 5AH4 · UniProt A0QND6
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