MolNFT v1 · #138349 · protein
Propionyl-dpsc in complex with oxetane-bearing probe
5WGC · Daunorubicin-doxorubicin polyketide synthase: “Propionyl-dpsc in complex with oxetane-bearing probe”. X-ray diffraction, 1 ligand (AFY), 5 pockets (best druggability 0.72). MolNFT v1 #138349 on GenesisL1: 3D structure, binding sites…
- PDB
- 5WGC
- Type
- protein
- Length
- 685 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Daunorubicin-doxorubicin polyketide synthase
- EC
- 2.3.1.-
- UniProt
- Q54816
- Ligands
- AFY
- Pockets
- 5 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Daunorubicin-doxorubicin polyketide synthase (EC 2.3.1.-) | protein | 342 | 41% helix, 23% strand | Q54816 |
| B | Daunorubicin-doxorubicin polyketide synthase (EC 2.3.1.-) | protein | 343 | 40% helix, 23% strand | Q54816 |
Ligands and binding sites
- AFY · (3-{[2-({N-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino) ethyl]sulfanyl}oxetan-3-yl)acetic acid · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 331 | 0.72 | 0.85 | 60 | empty |
| 2 | 362 | 0.70 | 0.83 | 40 | AFY |
| 3 | 391 | 0.68 | 0.80 | 35 | AFY |
| 4 | 76 | 0.30 | 0.73 | 23 | empty |
| 5 | 52 | 0.24 | 0.73 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 2855 Ų buried · 22 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (nonstandard).
Compared structures
- 5WGC · propionyl-DpsC in complex with oxetane-bearing probe · 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 Q54816
- Elsewhere: RCSB PDB 5WGC · PDBe 5WGC · UniProt Q54816
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