MolNFT v1 · #138664 · protein
Structure of fungal meroterpenoid isomerase TRT14 complexed with substrate analog and endo-terretonin D
5WQH: “Structure of fungal meroterpenoid isomerase TRT14 complexed with substrate analog and endo-terretonin D”. X-ray diffraction, 3 ligands (7WU, 7WX, CA), 17 pockets (best druggability 0.78). MolNFT v1 #138664 on GenesisL1: 3D…
- PDB
- 5WQH
- Type
- protein
- Length
- 840 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Isomerase TRT14
- UniProt
- Q0C8A2
- Ligands
- 7WU, 7WX, CA
- Pockets
- 17 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 34% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Isomerase TRT14 | protein | 140 | 34% helix, 39% strand | Q0C8A2 |
Ligands and binding sites
- 7WU · Methyl (2s,4ar,4bs,5s,6as,10as,10bs,12as)-2,4B,7,7,10A, 12,12A-heptamethyl-5-oxidanyl-1,4,6,8-tetrakis(oxidanylidene)-4A,5,6A,9,10,10B-hexahydronaphtho[1,2-h]isochromene-2-carboxylate · ligand · 4 copies · chains A, B, C, F
- 7WX · methyl (5S,7S,8S,9S,10S,13R,14R,16S)-4,4,8,10,12,13,16-heptamethyl-7,16-bis(oxidanyl)-3,6,15,17-tetrakis(oxidanylidene)-2,5,7,9-tetrahydro-1H-cyclopenta[a]phenanthrene-14-carboxylate · ligand · 2 copies · chains D, E
- CA · Calcium ion · metal · 7 copies · chains A, B, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 403 | 0.78 | 0.87 | 34 | 7WX |
| 2 | 381 | 0.78 | 0.87 | 34 | 7WU |
| 3 | 408 | 0.78 | 0.86 | 33 | 7WX |
| 4 | 393 | 0.77 | 0.86 | 30 | 7WU |
| 5 | 428 | 0.77 | 0.85 | 36 | 7WU |
Interfaces
7 interfaces between chains.
- E–F · 1265 Ų buried · 29 hydrogen bonds · protein-protein
- A–C · 1189 Ų buried · 30 hydrogen bonds · protein-protein
- B–D · 1183 Ų buried · 28 hydrogen bonds · protein-protein
- A–B · 544 Ų buried · 5 hydrogen bonds · protein-protein
- D–E · 232 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 5WQH · Structure of fungal meroterpenoid isomerase Trt14 complexed with substrate analog and… · the same entry in another collection · chain C against C, TM-score 1.00
- Q0C8A2 · AlphaFold monomer V2.0 prediction for isomerase TRT14 (Q0C8A2) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 Q0C8A2
- Elsewhere: RCSB PDB 5WQH · PDBe 5WQH · UniProt Q0C8A2
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