MolNFT v1 · #138663 · protein
Structure of fungal meroterpenoid isomerase TRT14 complexed with terretonin D
5WQG: “Structure of fungal meroterpenoid isomerase TRT14 complexed with terretonin D”. X-ray diffraction, 2 ligands (7MI, CA), 16 pockets (best druggability 0.79). MolNFT v1 #138663 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 5WQG
- Type
- protein
- Length
- 837 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Isomerase TRT14
- EC
- 5.-.-.-
- UniProt
- Q0C8A2
- Ligands
- 7MI, CA
- Pockets
- 16 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D | Isomerase TRT14 (EC 5.-.-.-) | protein | 140 | 36% helix, 39% strand | Q0C8A2 |
| B, E, F | Isomerase TRT14 (EC 5.-.-.-) | protein | 139 | 37% helix, 37% strand | Q0C8A2 |
Ligands and binding sites
- 7MI · Methyl (2s,4ar,4bs,5s,6as,10as,10bs,12as)-2,4B,7,7,10A, 12A-hexamethyl-12-methylidene-5-oxidanyl-1,4,6,8-tetrakis(oxidanylidene)-5,6A,9,10,10B,11-hexahydro-4AH-naphtho[1,2-h]isochromene-2-carboxylate · ligand · 3 copies · chains C, D, F
- CA · Calcium ion · metal · 6 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 371 | 0.79 | 0.87 | 32 | 7MI |
| 2 | 391 | 0.78 | 0.87 | 34 | empty |
| 3 | 403 | 0.78 | 0.87 | 33 | 7MI |
| 4 | 394 | 0.78 | 0.86 | 31 | 7MI |
| 5 | 374 | 0.77 | 0.86 | 34 | empty |
Interfaces
7 interfaces between chains.
- E–F · 1237 Ų buried · 32 hydrogen bonds · protein-protein
- B–D · 1214 Ų buried · 29 hydrogen bonds · protein-protein
- A–C · 1200 Ų buried · 27 hydrogen bonds · protein-protein
- A–B · 517 Ų buried · 4 hydrogen bonds · protein-protein
- D–E · 193 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 5WQG · Structure of fungal meroterpenoid isomerase Trt14 complexed with terretonin D · the same entry in another collection · chain F against F, 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 0.99
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 5WQG · PDBe 5WQG · UniProt Q0C8A2
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