MolNFT v1 · #120052 · protein

Cytochrome P450 vdh (CYP107BR1) L348M mutant

5GNM · Vitamin D(3) 25-hydroxylase: “Cytochrome P450 vdh (CYP107BR1) L348M mutant”. X-ray diffraction, 1 ligand (HEM), 17 pockets (best druggability 0.82). MolNFT v1 #120052 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5GNM
Type: protein
Length: 1,600 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Vitamin D(3) 25-hydroxylase
EC: 1.14.15.15
UniProt: C4B644
Ligands: HEM
Pockets: 17 · best druggability 0.82

Structure

x-ray diffraction · 2 distinct chains · 51% helix, 10% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Vitamin D(3) 25-hydroxylase (EC 1.14.15.15)	protein	399	51% helix, 10% strand	C4B644
C, D	Vitamin D(3) 25-hydroxylase (EC 1.14.15.15)	protein	401	50% helix, 10% strand	C4B644

Ligands and binding sites

HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains A, B, C, D

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

17 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	712	0.82	0.86	96	empty
2	504	0.81	0.88	61	HEM
3	746	0.79	0.83	72	HEM
4	738	0.79	0.83	76	HEM
5	612	0.78	0.83	61	HEM

Interfaces

5 interfaces between chains.

A–D · 711 Å² buried · 9 hydrogen bonds · protein-protein
A–B · 711 Å² buried · 4 hydrogen bonds · protein-protein
B–C · 590 Å² buried · 9 hydrogen bonds · protein-protein
A–C · 548 Å² buried · 5 hydrogen bonds · protein-protein
C–D · 267 Å² buried · 2 hydrogen bonds · protein-protein

Compared structures

5GNM · Cytochrome P450 Vdh (CYP107BR1) L348M mutant · the same entry in another collection · chain D against D, 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 B against A, TM-score 0.95

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 5GNM · PDBe 5GNM · UniProt C4B644

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