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A complex of a new GH20 enzyme from bacteroides thetaiotaomicron

Analyse A complex of a new GH20 enzyme from bacteroides thetaiotaomicron in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7DVB
Type: protein
Length: 2,052 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Beta-N-acetylhexosaminidase
EC: 3.2.1.52
UniProt: A0A0P0FIE8
Ligands: Q4Z, NGS
Pockets: 12 · best druggability 0.78

Structure

x-ray diffraction · 4 distinct chains · 38% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Beta-N-acetylhexosaminidase (EC 3.2.1.52)	protein	507	38% helix, 19% strand	A0A0P0FIE8
B	Beta-N-acetylhexosaminidase (EC 3.2.1.52)	protein	508	38% helix, 19% strand	A0A0P0FIE8
C	Beta-N-acetylhexosaminidase (EC 3.2.1.52)	protein	519	38% helix, 18% strand	A0A0P0FIE8
D	Beta-N-acetylhexosaminidase (EC 3.2.1.52)	protein	518	38% helix, 19% strand	A0A0P0FIE8

Ligands and binding sites

Q4Z · [(3~{a}~{R},5~{R},6~{S},7~{R},7~{a}~{R})-2-methyl-6,7-bis(oxidanyl)-5,6,7,7~{a}-tetrahydro-3~{a}~{H}-pyrano[3,2-d][1,3]oxazol-1-ium-5-yl]methyl sulfate · ligand · 4 copies · chains A, B, C, D
NGS · 2-acetamido-2-deoxy-6-O-sulfo-beta-D-glucopyranose · ligand · chains D

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

Pockets

12 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	617	0.78	0.83	59	empty
2	911	0.78	0.80	112	empty
3	599	0.73	0.80	69	empty
4	98	0.55	0.84	17	Q4Z
5	177	0.53	0.79	25	Q4Z

Interfaces

4 interfaces between chains.

B–D · 866 Å² buried · 9 hydrogen bonds · protein-protein
A–C · 381 Å² buried · 0 hydrogen bonds · protein-protein
B–C · 339 Å² buried · 2 hydrogen bonds · protein-protein
A–B · 75 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

7DVB · D335N variant of Bt4394 in complex with 6SO3-NAG-oxazoline intermediate · the same entry in another collection · 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 A0A0P0FIE8
Elsewhere: RCSB PDB 7DVB · PDBe 7DVB · UniProt A0A0P0FIE8

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