MolNFT v1 · #155316 · protein
Crystal structure of the acyltransferase domain from the third module of the ansamitocin polyketide synthase
6L3M: “Crystal structure of the acyltransferase domain from the third module of the ansamitocin polyketide synthase”. X-ray diffraction, 2 ligands (E5U, PO4), 18 pockets (best druggability 0.66). MolNFT v1 #155316 on GenesisL1: 3D…
- 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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