MolNFT v1 · #83114 · protein

Human alpha-L-iduronidase

3W81: “Human alpha-L-iduronidase”. X-ray diffraction, 8 ligands (NAG, MAN, BMA), 13 pockets (best druggability 0.69). MolNFT v1 #83114 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 3W81
Type: protein
Length: 1,232 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Alpha-L-iduronidase
EC: 3.2.1.76
UniProt: P35475
Ligands: NAG, MAN, BMA, GAL, FUC, PO4, CL, PO3
Pockets: 13 · best druggability 0.69

Structure

x-ray diffraction · 1 distinct chain · 26% helix, 30% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Alpha-L-iduronidase (EC 3.2.1.76)	protein	616	26% helix, 30% strand	P35475

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 14 copies · chains A, B
MAN · alpha-D-mannopyranose · sugar · 14 copies · chains A, B
BMA · beta-D-mannopyranose · sugar · 3 copies · chains A, B
GAL · beta-D-galactopyranose · sugar
FUC · alpha-L-fucopyranose · sugar
PO4 · Phosphate ion · ion · 4 copies · chains A, B
CL · Chloride ion · ion · 2 copies · chains A, B
PO3 · Phosphite ion · ion · chains B
TLA · L(+)-tartaric acid · additive · 4 copies · chains A, B
GOL · Glycerol · additive · 2 copies · chains A, B

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

Pockets

13 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	57	0.69	0.97	21	empty
2	503	0.65	0.77	64	NAG
3	207	0.58	0.80	25	empty
4	144	0.52	0.80	22	empty
5	148	0.50	0.79	23	PO3

Interfaces

1 interface between chains.

A–B · 237 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 glycan, 2 disulfide (N-glycosylation, disulfide).

Compared structures

3W81 · Human alpha-l-iduronidase · the same entry in another collection · chain A against A, TM-score 1.00
P35475 · AlphaFold monomer V2.0 prediction for alpha-L-iduronidase (P35475) · a predicted model of the same protein · 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 P35475
Elsewhere: RCSB PDB 3W81 · PDBe 3W81 · UniProt P35475

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.