MolNFT v1 · #160502 · protein

Crystal structure of the core catalytic domain of human O-glcnacase bound to mk-8719

6PM9 · O-glcnacase tim-barrel domain: “Crystal structure of the core catalytic domain of human O-glcnacase bound to mk-8719”. X-ray diffraction, 1 ligand (OQ1), 20 pockets (best druggability 0.77). MolNFT v1 #160502 on GenesisL1: 3D…

PDB: 6PM9
Type: protein
Length: 1,688 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: O-glcnacase tim-barrel domain; O-glcnacase stalk domain
EC: 3.2.1.169
UniProt: O60502
Ligands: OQ1
Pockets: 20 · best druggability 0.77

Structure

x-ray diffraction · 7 distinct chains · 49% helix, 9% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	O-glcnacase tim-barrel domain (EC 3.2.1.169)	protein	309	39% helix, 13% strand	O60502
C	O-glcnacase tim-barrel domain (EC 3.2.1.169)	protein	310	38% helix, 12% strand	O60502
D	O-glcnacase tim-barrel domain (EC 3.2.1.169)	protein	310	40% helix, 12% strand	O60502
E	O-glcnacase stalk domain (EC 3.2.1.169)	protein	112	71% helix, 0% strand	O60502
F	O-glcnacase stalk domain (EC 3.2.1.169)	protein	109	75% helix, 1% strand	O60502
G	O-glcnacase stalk domain (EC 3.2.1.169)	protein	117	68% helix, 1% strand	O60502
H	O-glcnacase stalk domain (EC 3.2.1.169)	protein	112	71% helix, 2% strand	O60502

Ligands and binding sites

OQ1 · (3ar,5s,6s,7r,7ar)-5-(difluoromethyl)-2-(ethylamino)-5, 6,7,7A-tetrahydro-3AH-pyrano[3,2-d][1,3]thiazole-6,7-diol · ligand · 4 copies · chains A, G, B, C, E, D, H

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

Pockets

20 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	835	0.77	0.81	73	empty
2	234	0.76	0.90	36	empty
3	239	0.73	0.87	35	empty
4	857	0.71	0.77	65	empty
5	414	0.67	0.79	37	empty

Interfaces

19 interfaces between chains.

B–G · 1505 Å² buried · 21 hydrogen bonds · protein-protein
A–F · 1453 Å² buried · 20 hydrogen bonds · protein-protein
D–E · 1306 Å² buried · 13 hydrogen bonds · protein-protein
E–H · 1283 Å² buried · 1 hydrogen bond · protein-protein
C–H · 1281 Å² buried · 13 hydrogen bonds · protein-protein

Compared structures

6PM9 · Crystal structure of the core catalytic domain of human O-GlcNAcase bound to MK-8719 · the same entry in another collection · chain H against H, TM-score 1.00
O60502 · AlphaFold monomer V2.0 prediction for protein O-glcnacase (O60502) · 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 O60502
Elsewhere: RCSB PDB 6PM9 · PDBe 6PM9 · UniProt O60502

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