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Crystal structure of mtb PKS13 thioesterase domain in complex with inhibitor TAM6
Analyse Crystal structure of mtb PKS13 thioesterase domain in complex with inhibitor… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5V40
- Type
- protein
- Length
- 548 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Polyketide synthase PKS13 (termination polyketide synthase)
- EC
- 2.7.7.-
- UniProt
- A0A0T9CRX1
- Ligands
- JS1
- Pockets
- 9 · best druggability 0.70
Structure
x-ray diffraction · 2 distinct chains · 46% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Polyketide synthase PKS13 (termination polyketide synthase) (EC 2.7.7.-) | protein | 273 | 46% helix, 14% strand | A0A0T9CRX1 |
| B | Polyketide synthase PKS13 (termination polyketide synthase) (EC 2.7.7.-) | protein | 275 | 45% helix, 15% strand | A0A0T9CRX1 |
Ligands and binding sites
- JS1 · ethyl 4-[(dimethylamino)methyl]-5-hydroxy-2-phenyl-1-benzofuran-3-carboxylate · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 499 | 0.70 | 0.80 | 52 | JS1 |
| 2 | 556 | 0.69 | 0.78 | 49 | JS1 |
| 3 | 400 | 0.59 | 0.75 | 35 | empty |
| 4 | 161 | 0.46 | 0.76 | 29 | empty |
| 5 | 116 | 0.42 | 0.76 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 590 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 5V40 · Crystal Structure of Mtb Pks13 Thioesterase domain in complex with inhibitor TAM6 · 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 A0A0T9CRX1
- Elsewhere: RCSB PDB 5V40 · PDBe 5V40 · UniProt A0A0T9CRX1
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