MolNFT v1 · #113305 · protein

Structure of GH84 with ligand

5ABH · O-glcnacase BT_4395: “Structure of GH84 with ligand”. X-ray diffraction, 3 ligands (YWN, CA, CL), 20 pockets (best druggability 0.69). MolNFT v1 #113305 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5ABH
Type: protein
Length: 1,346 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: O-glcnacase BT_4395
EC: 3.2.1.169, 3.2.1.52
UniProt: Q89ZI2
Ligands: YWN, CA, CL
Pockets: 20 · best druggability 0.69

Structure

x-ray diffraction · 2 distinct chains · 40% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	O-glcnacase BT_4395 (EC 3.2.1.169, 3.2.1.52)	protein	677	40% helix, 19% strand	Q89ZI2
B	O-glcnacase BT_4395 (EC 3.2.1.169, 3.2.1.52)	protein	669	39% helix, 20% strand	Q89ZI2

Ligands and binding sites

YWN · 2-[(2R,3S,4R,5R)-5-(hydroxymethyl)-3,4-bis(oxidanyl)-1-pentyl-pyrrolidin-2-yl]-N-methyl-ethanamide · ligand · 2 copies · chains A, B
CA · Calcium ion · metal · chains B
CL · Chloride ion · ion · chains A
EDO · 1,2-ethanediol · additive · 2 copies · chains A, B

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

Pockets

20 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	516	0.69	0.79	48	empty
2	504	0.67	0.78	57	empty
3	233	0.59	0.79	25	empty
4	262	0.59	0.79	31	empty
5	91	0.56	0.85	19	YWN

Interfaces

1 interface between chains.

A–B · 1098 Å² buried · 23 hydrogen bonds · protein-protein

Compared structures

5ABH · Structure of GH84 with ligand · the same entry in another collection · chain A against A, TM-score 1.00
Q89ZI2 · AlphaFold monomer V2.0 prediction for O-glcnacase BT_4395 (Q89ZI2) · 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 Q89ZI2
Elsewhere: RCSB PDB 5ABH · PDBe 5ABH · UniProt Q89ZI2

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