MolNFT v1 · #124318 · protein

The crystal structure of an alpha-mannosidase from enterococcus faecalis V583

5KBP · Glycosyl hydrolase, family 38: “The crystal structure of an alpha-mannosidase from enterococcus faecalis V583”. X-ray diffraction, 1 ligand (SO4), 20 pockets (best druggability 0.81). MolNFT v1 #124318 on GenesisL1: 3D structure…

PDB: 5KBP
Type: protein
Length: 1,770 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Glycosyl hydrolase, family 38
UniProt: Q834E8
Ligands: SO4
Pockets: 20 · best druggability 0.81

Structure

x-ray diffraction · 2 distinct chains · 25% helix, 33% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Glycosyl hydrolase, family 38	protein	886	26% helix, 33% strand	Q834E8
B	Glycosyl hydrolase, family 38	protein	884	25% helix, 33% strand	Q834E8

Ligands and binding sites

SO4 · Sulfate ion · ion · 24 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, 14 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1181	0.81	0.82	84	SO4
2	92	0.78	0.99	29	empty
3	86	0.76	0.98	20	empty
4	59	0.70	0.97	14	empty
5	445	0.68	0.79	56	empty

Interfaces

1 interface between chains.

A–B · 2994 Å² buried · 30 hydrogen bonds · protein-protein

Compared structures

5KBP · The crystal structure of an alpha-mannosidase from Enterococcus faecalis V583 · 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 Q834E8
Elsewhere: RCSB PDB 5KBP · PDBe 5KBP · UniProt Q834E8

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