Research workbench

PR3 (myeloblastin)

Analyse PR3 (myeloblastin) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1FUJ
Type: protein
Length: 884 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: PR3
UniProt: P24158
Ligands: NAG, FUC
Pockets: 5 · best druggability 0.84

Structure

x-ray diffraction · 1 distinct chain · 9% helix, 38% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	PR3	protein	221	9% helix, 38% strand	P24158

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, B, C, D
FUC · alpha-L-fucopyranose · sugar · 4 copies · chains A, B, C, D

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

Pockets

5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1012	0.84	0.84	89	empty
2	971	0.83	0.84	90	empty
3	87	0.35	0.75	19	empty
4	56	0.28	0.74	22	empty
5	50	0.25	0.73	18	empty

Interfaces

4 interfaces between chains.

C–D · 792 Å² buried · 6 hydrogen bonds · protein-protein
A–B · 715 Å² buried · 8 hydrogen bonds · protein-protein
B–C · 492 Å² buried · 3 hydrogen bonds · protein-protein
A–D · 391 Å² buried · 2 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 16 disulfide, 4 glycan (disulfide, N-glycosylation).

Compared structures

1FUJ · PR3 (myeloblastin) · the same entry in another collection · chain B against B, TM-score 1.00
P24158 · AlphaFold monomer V2.0 prediction for myeloblastin (P24158) · a predicted model of the same protein · chain A against A, TM-score 0.99

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 P24158
Elsewhere: RCSB PDB 1FUJ · PDBe 1FUJ · UniProt P24158

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