MolNFT v1 · #159431 · protein
Crystal structure of piper methysticum styrylpyrone synthase 1 in complex with P-coumaroyl-CoA
6OP5: “Crystal structure of piper methysticum styrylpyrone synthase 1 in complex with P-coumaroyl-CoA”. X-ray diffraction, 1 ligand (WCA), 17 pockets (best druggability 0.87). MolNFT v1 #159431 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6OP5
- Type
- protein
- Length
- 2,293 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Styrylpyrone synthase 1
- UniProt
- A0A384E132
- Ligands
- WCA
- Pockets
- 17 · best druggability 0.87
Structure
x-ray diffraction · 3 distinct chains · 39% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Styrylpyrone synthase 1 | protein | 383 | 39% helix, 24% strand | A0A384E132 |
| B, D, E, F | Styrylpyrone synthase 1 | protein | 382 | 39% helix, 24% strand | A0A384E132 |
| C | Styrylpyrone synthase 1 | protein | 382 | 38% helix, 24% strand | A0A384E132 |
Ligands and binding sites
- WCA · p-coumaroyl-CoA · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1018 | 0.87 | 0.88 | 105 | empty |
| 2 | 1169 | 0.86 | 0.87 | 108 | empty |
| 3 | 433 | 0.80 | 0.88 | 51 | WCA |
| 4 | 413 | 0.75 | 0.85 | 42 | WCA |
| 5 | 584 | 0.73 | 0.80 | 47 | empty |
Interfaces
8 interfaces between chains.
- A–B · 2610 Ų buried · 47 hydrogen bonds · protein-protein
- E–F · 769 Ų buried · 11 hydrogen bonds · protein-protein
- C–D · 761 Ų buried · 13 hydrogen bonds · protein-protein
- A–E · 342 Ų buried · 4 hydrogen bonds · protein-protein
- D–F · 310 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent, 1 modified (covalent ligand, nonstandard).
Compared structures
- 6OP5 · Crystal Structure of Piper methysticum Styrylpyrone Synthase 1 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
- Every structure of UniProt A0A384E132
- Elsewhere: RCSB PDB 6OP5 · PDBe 6OP5 · UniProt A0A384E132
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