MolNFT v1 · #113485 · protein
The sliding clamp of mycobacterium tuberculosis in complex with a natural product.
5AGV · DNA polymerase III subunit beta: “The sliding clamp of mycobacterium tuberculosis in complex with a natural product.”. X-ray diffraction, 3 ligands (ACE, NA, CA), 6 pockets (best druggability 0.72). MolNFT v1 #113485 on GenesisL1…
- PDB
- 5AGV
- Type
- protein
- Length
- 803 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
- I6XU56
- Ligands
- ACE, NA, CA
- Pockets
- 6 · best druggability 0.72
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 | 390 | 22% helix, 43% strand | I6XU56 |
| B | DNA polymerase III subunit beta (EC 2.7.7.7) | protein | 393 | 20% helix, 42% strand | I6XU56 |
| C, D | Cyclohexyl griselimycin | protein | 10 | 0% helix, 0% strand | — |
Ligands and binding sites
- ACE · Acetyl group · ligand · 2 copies · chains A, C, B, D
- NA · Sodium ion · metal · 12 copies · chains A, B
- CA · Calcium ion · metal · 6 copies · chains A, B
- BU3 · (R,R)-2,3-butanediol · additive · 5 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 788 | 0.72 | 0.78 | 89 | NA, CA, BU3 |
| 2 | 96 | 0.64 | 0.90 | 25 | NA, BU3 |
| 3 | 411 | 0.63 | 0.77 | 45 | BU3, NA |
| 4 | 112 | 0.56 | 0.84 | 22 | CA, BU3 |
| 5 | 170 | 0.46 | 0.76 | 29 | empty |
Interfaces
3 interfaces between chains.
- A–B · 793 Ų buried · 16 hydrogen bonds · protein-protein
- A–C · 734 Ų buried · 5 hydrogen bonds · protein-protein
- B–D · 729 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 modified, 2 covalent (nonstandard, methylation, covalent ligand).
Compared structures
- 5AGV · 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 5AGV · PDBe 5AGV · UniProt I6XU56
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