Research workbench
Crystal structure of cyclo-L-TRP-L-pro-bound cytochrome P450 NASF5053 from streptomyces sp. nrrl F-5053
Analyse Crystal structure of cyclo-L-TRP-L-pro-bound cytochrome P450 NASF5053 from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6VXV
- Type
- protein
- Length
- 395 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cytochrome P450 NASF5053
- EC
- 1.14.-.-
- Ligands
- QRP, HEM, NA, CA
- Pockets
- 3 · best druggability 0.86
Structure
x-ray diffraction · 1 distinct chain · 51% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cytochrome P450 NASF5053 (EC 1.14.-.-) | protein | 395 | 51% helix, 11% strand | — |
Ligands and binding sites
- QRP · (3S,8aS)-3-(1H-indol-3-ylmethyl)hexahydropyrrolo[1,2-a]pyrazine-1,4-dione · ligand · 2 copies · chains A
- HEM · Protoporphyrin IX containing Fe · ligand · chains A
- NA · Sodium ion · metal · chains A
- CA · Calcium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 976 | 0.86 | 0.86 | 83 | QRP, HEM |
| 2 | 125 | 0.51 | 0.81 | 23 | empty |
| 3 | 78 | 0.38 | 0.78 | 18 | empty |
Compared structures
- 6VXV · Crystal structure of cyclo-L-Trp-L-Pro-bound cytochrome P450 NasF5053 from Streptomyces… · 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
- Elsewhere: RCSB PDB 6VXV · PDBe 6VXV
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.