Research workbench
Crystal structure of the acyltransferase domain from the third module of the ansamitocin polyketide synthase
Analyse Crystal structure of the acyltransferase domain from the third module of the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6L3M
- Type
- protein
- Length
- 1,678 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Polyketide synthase
- Ligands
- E5U, PO4
- Pockets
- 18 · best druggability 0.66
Structure
x-ray diffraction · 2 distinct chains · 46% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Polyketide synthase | protein | 419 | 46% helix, 16% strand | — |
| B, D | Polyketide synthase | protein | 420 | 46% helix, 16% strand | — |
Ligands and binding sites
- E5U · 2-methoxypropanedioic acid · ligand · 4 copies · chains A, B, C, D
- PO4 · Phosphate ion · ion · 6 copies · chains A, B, C, D
- GOL · Glycerol · additive · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 135 | 0.66 | 0.88 | 38 | GOL, E5U |
| 2 | 125 | 0.64 | 0.87 | 40 | GOL, E5U |
| 3 | 117 | 0.63 | 0.88 | 38 | GOL, E5U |
| 4 | 116 | 0.63 | 0.88 | 37 | GOL, E5U |
| 5 | 58 | 0.54 | 0.88 | 23 | empty |
Interfaces
3 interfaces between chains.
- B–D · 495 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 463 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 407 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent (covalent ligand).
Compared structures
- 6L3M · Crystal Structure of the acyltransferase domain from the third module of the ansamitocin… · 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
- Elsewhere: RCSB PDB 6L3M · PDBe 6L3M
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