Research workbench
Structure of cytochrome P450 vdh from pseudonocardia autotrophica (trigonal crystal form)
Analyse Structure of cytochrome P450 vdh from pseudonocardia autotrophica (trigonal… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3A4G
- Type
- protein
- Length
- 395 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Vitamin D hydroxylase
- UniProt
- C4B644
- Ligands
- HEM
- Pockets
- 4 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 50% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Vitamin D hydroxylase | protein | 395 | 50% helix, 10% strand | C4B644 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · chains A
- PG0 · 2-(2-methoxyethoxy)ethanol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 712 | 0.78 | 0.82 | 73 | HEM, PG0 |
| 2 | 64 | 0.46 | 0.83 | 18 | empty |
| 3 | 93 | 0.42 | 0.78 | 16 | empty |
| 4 | 51 | 0.31 | 0.77 | 13 | empty |
Compared structures
- 3A4G · Structure of cytochrome P450 vdh from Pseudonocardia autotrophica (trigonal crystal form) · the same entry in another collection · chain A against A, TM-score 1.00
- C4B644 · AlphaFold monomer V2.0 prediction for vitamin D(3) 25-hydroxylase (C4B644) · a predicted model of the same protein · chain A against A, TM-score 0.93
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 C4B644
- Elsewhere: RCSB PDB 3A4G · PDBe 3A4G · UniProt C4B644
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