Research workbench
Crystal structure of a fragment containing the acyltransferase domain of PKS13 from mycobacterium tuberculosis in the carboxypalmitoylated form at 2.5 a
Analyse Crystal structure of a fragment containing the acyltransferase domain of PKS13… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3TZZ
- Type
- protein
- Length
- 938 residues
- Chains
- 3
- 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
- XPM, SO4
- Pockets
- 11 · best druggability 0.72
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 | 463 | 49% helix, 14% strand | O53579 |
| B | Polyketide synthase PKS13 (EC 2.3.1.-) | protein | 465 | 49% helix, 14% strand | O53579 |
| C | 12-mer peptide | protein | 10 | 0% helix, 20% strand | — |
Ligands and binding sites
- XPM · tetradecylpropanedioic acid · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 2 copies · chains B, C
- GOL · Glycerol · additive · 7 copies · chains A, B
- PG0 · 2-(2-methoxyethoxy)ethanol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 308 | 0.72 | 0.85 | 43 | XPM, GOL |
| 2 | 183 | 0.68 | 0.87 | 33 | XPM |
| 3 | 168 | 0.55 | 0.80 | 35 | empty |
| 4 | 229 | 0.50 | 0.75 | 27 | empty |
| 5 | 185 | 0.48 | 0.76 | 27 | empty |
Interfaces
1 interface between chains.
- B–C · 468 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 3TZZ · 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 3TZZ · PDBe 3TZZ · UniProt O53579
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