MolNFT v1 · #153885 · protein

Crystal structure of native nagz from neisseria gonorrhoeae

6JTI · Beta-hexosaminidase: “Crystal structure of native nagz from neisseria gonorrhoeae”. X-ray diffraction, 20 pockets (best druggability 0.83). MolNFT v1 #153885 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6JTI
Type: protein
Length: 2,049 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Beta-hexosaminidase
EC: 3.2.1.52
UniProt: Q5FA94
Pockets: 20 · best druggability 0.83

Structure

x-ray diffraction · 6 distinct chains · 44% helix, 14% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Beta-hexosaminidase (EC 3.2.1.52)	protein	339	45% helix, 14% strand	Q5FA94
B	Beta-hexosaminidase (EC 3.2.1.52)	protein	344	44% helix, 14% strand	Q5FA94
C	Beta-hexosaminidase (EC 3.2.1.52)	protein	343	44% helix, 13% strand	Q5FA94
D	Beta-hexosaminidase (EC 3.2.1.52)	protein	344	44% helix, 14% strand	Q5FA94
E	Beta-hexosaminidase (EC 3.2.1.52)	protein	339	45% helix, 14% strand	Q5FA94
F	Beta-hexosaminidase (EC 3.2.1.52)	protein	340	44% helix, 14% strand	Q5FA94

Pockets

20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	641	0.83	0.87	86	empty
2	639	0.76	0.82	75	empty
3	508	0.75	0.83	62	empty
4	495	0.73	0.82	55	empty
5	727	0.69	0.76	65	empty

Interfaces

7 interfaces between chains.

A–C · 1483 Å² buried · 30 hydrogen bonds · protein-protein
D–E · 1459 Å² buried · 27 hydrogen bonds · protein-protein
B–F · 1434 Å² buried · 24 hydrogen bonds · protein-protein
B–D · 514 Å² buried · 12 hydrogen bonds · protein-protein
A–B · 276 Å² buried · 2 hydrogen bonds · protein-protein

Compared structures

6JTI · Crystal structure of native NagZ from Neisseria gonorrhoeae · the same entry in another collection · chain F against F, TM-score 1.00
Q5FA94 · AlphaFold monomer V2.0 prediction for beta-hexosaminidase (Q5FA94) · a predicted model of the same protein · chain E 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 Q5FA94
Elsewhere: RCSB PDB 6JTI · PDBe 6JTI · UniProt Q5FA94

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