MolNFT v1 · #112217 · protein

Human dopamine beta-hydroxylase

4ZEL: “Human dopamine beta-hydroxylase”. X-ray diffraction, 4 ligands (NAG, BMA, MAN), 16 pockets (best druggability 0.72). MolNFT v1 #112217 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4ZEL
Type: protein
Length: 1,094 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Dopamine beta-hydroxylase
EC: 1.14.17.1
UniProt: P09172
Ligands: NAG, BMA, MAN, CU
Pockets: 16 · best druggability 0.72

Structure

x-ray diffraction · 2 distinct chains · 7% helix, 43% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Dopamine beta-hydroxylase (EC 1.14.17.1)	protein	550	7% helix, 43% strand	P09172
B	Dopamine beta-hydroxylase (EC 1.14.17.1)	protein	544	6% helix, 44% strand	P09172

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 10 copies · chains A, B
BMA · beta-D-mannopyranose · sugar · 3 copies
MAN · alpha-D-mannopyranose · sugar
CU · Copper (II) ion · metal · chains A

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

Pockets

16 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	425	0.72	0.83	51	CU
2	60	0.67	0.95	19	empty
3	621	0.65	0.75	62	empty
4	233	0.63	0.82	40	empty
5	318	0.60	0.78	34	empty

Interfaces

1 interface between chains.

A–B · 1149 Å² buried · 5 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 13 disulfide, 6 glycan (disulfide, N-glycosylation).

Compared structures

4ZEL · Human dopamine beta-hydroxylase · the same entry in another collection · chain A against A, TM-score 1.00
P09172 · AlphaFold monomer V2.0 prediction for dopamine beta-hydroxylase (P09172) · a predicted model of the same protein · chain A against A, TM-score 0.98

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 P09172
Elsewhere: RCSB PDB 4ZEL · PDBe 4ZEL · UniProt P09172

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