MolNFT v1 · #80540 · protein
Crystal structure of a fragment containing the acyltransferase domain of PKS13 from mycobacterium tuberculosis in the palmitoylated form at 2.2 a
3TZY · Polyketide synthase PKS13: “Crystal structure of a fragment containing the acyltransferase domain of PKS13 from mycobacterium…”. X-ray diffraction, 2 ligands (PLM, SO4), 11 pockets (best druggability 0.69). MolNFT v1 #80540 on…
- PDB
- 3TZY
- Type
- protein
- Length
- 950 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Polyketide synthase PKS13; 12-mer peptide
- EC
- 2.3.1.-
- UniProt
- O53579
- Ligands
- PLM, SO4
- Pockets
- 11 · best druggability 0.69
Structure
x-ray diffraction · 3 distinct chains · 48% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Polyketide synthase PKS13 (EC 2.3.1.-) | protein | 464 | 49% helix, 14% strand | O53579 |
| B | Polyketide synthase PKS13 (EC 2.3.1.-) | protein | 466 | 47% helix, 14% strand | O53579 |
| C, D | 12-mer peptide | protein | 10 | 0% helix, 20% strand | — |
Ligands and binding sites
- PLM · Palmitic acid · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 2 copies · chains B, C
- GOL · Glycerol · additive · 7 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 160 | 0.69 | 0.88 | 34 | PLM |
| 2 | 162 | 0.64 | 0.86 | 29 | PLM, GOL |
| 3 | 202 | 0.50 | 0.76 | 28 | empty |
| 4 | 206 | 0.48 | 0.75 | 27 | empty |
| 5 | 180 | 0.47 | 0.76 | 34 | empty |
Interfaces
3 interfaces between chains.
- B–C · 523 Ų buried · 3 hydrogen bonds · protein-protein
- A–D · 439 Ų buried · 4 hydrogen bonds · protein-protein
- B–D · 45 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 lipid (palmitoylation).
Compared structures
- 3TZY · Crystal structure of a fragment containing the acyltransferase domain of Pks13 from… · 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 O53579
- Elsewhere: RCSB PDB 3TZY · PDBe 3TZY · UniProt O53579
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