MolNFT v1 · #136787 · protein
Crystal structure of the apo form of thioesterase domain of mtb PKS13
5V3W · Polyketide synthase PKS13 (termination polyketide synthase): “Crystal structure of the apo form of thioesterase domain of mtb PKS13”. X-ray diffraction, 1 ligand (2Q5), 10 pockets (best druggability 0.68). MolNFT v1 #136787 on…
- PDB
- 5V3W
- Type
- protein
- Length
- 547 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
- 2Q5
- Pockets
- 10 · best druggability 0.68
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 | 277 | 46% helix, 15% strand | A0A0T9CRX1 |
| B | Polyketide synthase PKS13 (termination polyketide synthase) (EC 2.7.7.-) | protein | 270 | 46% helix, 16% strand | A0A0T9CRX1 |
Ligands and binding sites
- 2Q5 · (2R)-2-{[(2R)-2-{[(2S)-2-{[(2R)-2-hydroxypropyl]oxy}propyl]oxy}propyl]oxy}propan-1-ol · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 524 | 0.68 | 0.78 | 55 | 2Q5 |
| 2 | 532 | 0.66 | 0.77 | 45 | 2Q5 |
| 3 | 342 | 0.56 | 0.75 | 40 | empty |
| 4 | 81 | 0.41 | 0.78 | 17 | empty |
| 5 | 89 | 0.37 | 0.76 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 616 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 5V3W · Crystal Structure of the Apo form of Thioesterase domain of Mtb Pks13 · 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 5V3W · PDBe 5V3W · UniProt A0A0T9CRX1
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