MolNFT v1 · #153047 · protein
Anisodus acutangulus type III polyketide sythase AAPKS2 in complex with 4-carboxy-3-oxobutanoyl-CoA
6J1N · A. acutangulus PKS2: “Anisodus acutangulus type III polyketide sythase AAPKS2 in complex with 4-carboxy-3-oxobutanoyl-CoA”. X-ray diffraction, 1 ligand (B7X), 6 pockets (best druggability 0.71). MolNFT v1 #153047 on GenesisL1: 3D…
- PDB
- 6J1N
- Type
- protein
- Length
- 755 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- A. acutangulus PKS2
- Ligands
- B7X
- Pockets
- 6 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | A. acutangulus PKS2 | protein | 379 | 42% helix, 23% strand | — |
| B | A. acutangulus PKS2 | protein | 376 | 43% helix, 23% strand | — |
Ligands and binding sites
- B7X · (3R,5R,9R)-1-[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-4-hydroxy-3-(phosphonooxy)tetrahydrofuran-2-yl]-3,5,9-trihydroxy-8,8-dimethyl-10,14,19,21-tetraoxo-2,4,6-trioxa-18-thia-11,15-diaza-3,5-diphosphatricosan-23-oic acid 3,5-dioxide (non-preferred name) · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 54 | 0.71 | 0.98 | 21 | empty |
| 2 | 52 | 0.71 | 0.98 | 22 | empty |
| 3 | 253 | 0.65 | 0.82 | 33 | B7X |
| 4 | 234 | 0.64 | 0.82 | 34 | B7X |
| 5 | 130 | 0.45 | 0.78 | 28 | empty |
Interfaces
1 interface between chains.
- A–B · 2536 Ų buried · 55 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 6J1N · Anisodus acutangulus type III polyketide sythase AaPKS2 in complex with… · 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 6J1N · PDBe 6J1N
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