Research workbench
The sliding clamp of mycobacterium smegmatis in complex with a natural product.
Analyse The sliding clamp of mycobacterium smegmatis in complex with a natural product. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5AH2
- Type
- protein
- Length
- 1,558 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase III subunit beta; Griselimycin
- EC
- 2.7.7.7
- UniProt
- A0QND6
- Ligands
- ACE, NA
- Pockets
- 12 · best druggability 0.76
Structure
x-ray diffraction · 5 distinct chains · 22% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase III subunit beta (EC 2.7.7.7) | protein | 380 | 23% helix, 43% strand | A0QND6 |
| B | DNA polymerase III subunit beta (EC 2.7.7.7) | protein | 377 | 22% helix, 43% strand | A0QND6 |
| C | DNA polymerase III subunit beta (EC 2.7.7.7) | protein | 382 | 20% helix, 42% strand | A0QND6 |
| D | DNA polymerase III subunit beta (EC 2.7.7.7) | protein | 379 | 21% helix, 44% strand | A0QND6 |
| E, F, G, H | Griselimycin | protein | 10 | 0% helix, 0% strand | — |
Ligands and binding sites
- ACE · Acetyl group · ligand · 4 copies · chains A, D, E, B, C, F, G, H
- NA · Sodium ion · metal · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1012 | 0.76 | 0.78 | 143 | empty |
| 2 | 885 | 0.75 | 0.79 | 105 | empty |
| 3 | 242 | 0.50 | 0.75 | 44 | empty |
| 4 | 252 | 0.49 | 0.74 | 36 | ACE |
| 5 | 207 | 0.49 | 0.75 | 34 | ACE |
Interfaces
12 interfaces between chains.
- A–B · 1173 Ų buried · 21 hydrogen bonds · protein-protein
- C–D · 1123 Ų buried · 24 hydrogen bonds · protein-protein
- B–C · 819 Ų buried · 12 hydrogen bonds · protein-protein
- A–D · 778 Ų buried · 10 hydrogen bonds · protein-protein
- D–H · 628 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 24 modified, 4 covalent (nonstandard, methylation, covalent ligand).
Compared structures
- 5AH2 · The sliding clamp of Mycobacterium smegmatis in complex with a natural product. · the same entry in another collection · chain H against H, TM-score 1.00
- A0QND6 · AlphaFold monomer V2.0 prediction for beta sliding clamp (A0QND6) · a predicted model of the same protein · chain B 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 5AH2 · PDBe 5AH2 · UniProt A0QND6
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