MolNFT v1 · #113484 · protein
The sliding clamp of mycobacterium tuberculosis in complex with a natural product.
5AGU · DNA polymerase III subunit beta: “The sliding clamp of mycobacterium tuberculosis in complex with a natural product.”. X-ray diffraction, 1 ligand (ACE), 3 pockets (best druggability 0.61). MolNFT v1 #113484 on GenesisL1: 3D…
- PDB
- 5AGU
- Type
- protein
- Length
- 771 residues
- Chains
- 4
- 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
- I6XU56
- Ligands
- ACE
- Pockets
- 3 · best druggability 0.61
Structure
x-ray diffraction · 3 distinct chains · 22% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase III subunit beta (EC 2.7.7.7) | protein | 373 | 21% helix, 45% strand | I6XU56 |
| B | DNA polymerase III subunit beta (EC 2.7.7.7) | protein | 378 | 23% helix, 44% strand | I6XU56 |
| C, D | Griselimycin | protein | 10 | 0% helix, 0% strand | — |
Ligands and binding sites
- ACE · Acetyl group · ligand · 2 copies · chains A, C, B, D
- BU3 · (R,R)-2,3-butanediol · additive · chains A
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 55 | 0.61 | 0.93 | 19 | empty |
| 2 | 63 | 0.34 | 0.77 | 17 | TRS |
| 3 | 62 | 0.32 | 0.76 | 14 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1164 Ų buried · 23 hydrogen bonds · protein-protein
- B–D · 659 Ų buried · 1 hydrogen bond · protein-protein
- A–C · 620 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 12 modified, 2 covalent (nonstandard, methylation, covalent ligand).
Compared structures
- 5AGU · The sliding clamp of Mycobacterium tuberculosis in complex with a natural product. · 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 I6XU56
- Elsewhere: RCSB PDB 5AGU · PDBe 5AGU · UniProt I6XU56
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