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Crystal structure of wild type ogpa from akkermansia muciniphila in P 41 21 2

Analyse Crystal structure of wild type ogpa from akkermansia muciniphila in P 41 21 2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6Z2D
Type: protein
Length: 354 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: O-glycan protease
UniProt: B2UR60
Ligands: ZN
Pockets: 4 · best druggability 0.42

Structure

x-ray diffraction · 1 distinct chain · 27% helix, 31% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	O-glycan protease	protein	354	27% helix, 31% strand	B2UR60

Ligands and binding sites

ZN · Zinc ion · metal · 2 copies · chains A
EDO · 1,2-ethanediol · additive · 4 copies · chains A
PG4 · Tetraethylene glycol · additive · chains A
FMT · Formic acid · additive · chains A

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

Pockets

4 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	123	0.42	0.76	24	empty
2	144	0.42	0.75	26	empty
3	51	0.39	0.81	21	empty
4	67	0.33	0.76	17	EDO

Compared structures

6Z2D · Crystal structure of wild type OgpA from Akkermansia muciniphila in P 41 21 2 · 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 B2UR60
Elsewhere: RCSB PDB 6Z2D · PDBe 6Z2D · UniProt B2UR60

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