MolNFT v1 · #163117 · protein
Structure of catharanthine synthase - an alpha-beta hydrolase from catharanthus roseus with a cleaviminium intermediate bound
6RT8: “Structure of catharanthine synthase - an alpha-beta hydrolase from catharanthus roseus with a cleaviminium…”. X-ray diffraction, 1 ligand (KJE), 20 pockets (best druggability 0.76). MolNFT v1 #163117 on GenesisL1: 3D structure…
- PDB
- 6RT8
- Type
- protein
- Length
- 2,501 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Catharanthine synthase
- EC
- 4.-.-.-
- UniProt
- A0A2P1GIW2
- Ligands
- KJE
- Pockets
- 20 · best druggability 0.76
Structure
x-ray diffraction · 4 distinct chains · 33% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Catharanthine synthase (EC 4.-.-.-) | protein | 314 | 33% helix, 23% strand | A0A2P1GIW2 |
| E | Catharanthine synthase (EC 4.-.-.-) | protein | 305 | 34% helix, 25% strand | A0A2P1GIW2 |
| F, G | Catharanthine synthase (EC 4.-.-.-) | protein | 313 | 33% helix, 24% strand | A0A2P1GIW2 |
| H | Catharanthine synthase (EC 4.-.-.-) | protein | 314 | 32% helix, 24% strand | A0A2P1GIW2 |
Ligands and binding sites
- KJE · 18-carboxymethoxy-cleaviminium · ligand · 8 copies · chains A, B, C, D, E, F, G, H
- P6G · Hexaethylene glycol · additive · 4 copies · chains A, B, C, D, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 215 | 0.76 | 0.90 | 27 | KJE |
| 2 | 221 | 0.76 | 0.90 | 26 | KJE |
| 3 | 240 | 0.76 | 0.89 | 27 | KJE |
| 4 | 977 | 0.74 | 0.77 | 86 | empty |
| 5 | 219 | 0.74 | 0.88 | 26 | KJE |
Interfaces
9 interfaces between chains.
- C–D · 988 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 988 Ų buried · 11 hydrogen bonds · protein-protein
- G–H · 970 Ų buried · 11 hydrogen bonds · protein-protein
- E–F · 967 Ų buried · 10 hydrogen bonds · protein-protein
- A–H · 668 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 6RT8 · Structure of catharanthine synthase - an alpha-beta hydrolase from Catharanthus roseus… · 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 A0A2P1GIW2
- Elsewhere: RCSB PDB 6RT8 · PDBe 6RT8 · UniProt A0A2P1GIW2
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