MolNFT v1 · #96262 · protein

Structure of clostridium botulinum cmp N-glycosidase, bcmb

4JEN: “Structure of clostridium botulinum cmp N-glycosidase, bcmb”. X-ray diffraction, 1 ligand (PO4), 5 pockets (best druggability 0.38). MolNFT v1 #96262 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4JEN
Type: protein
Length: 354 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Cmp N-glycosidase
UniProt: A7FS24
Ligands: PO4
Pockets: 5 · best druggability 0.38

Structure

x-ray diffraction · 3 distinct chains · 50% helix, 20% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Cmp N-glycosidase	protein	119	50% helix, 20% strand	A7FS24
B	Cmp N-glycosidase	protein	122	49% helix, 20% strand	A7FS24
C	Cmp N-glycosidase	protein	113	50% helix, 21% strand	A7FS24

Ligands and binding sites

PO4 · Phosphate ion · ion · 3 copies · chains A, B, C

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

Pockets

5 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	117	0.38	0.74	18	empty
2	91	0.35	0.75	19	empty
3	80	0.33	0.75	18	empty
4	70	0.30	0.73	20	PO4
5	50	0.26	0.74	16	empty

Interfaces

3 interfaces between chains.

A–B · 1357 Å² buried · 7 hydrogen bonds · protein-protein
A–C · 165 Å² buried · 1 hydrogen bond · protein-protein
B–C · 37 Å² buried · 1 hydrogen bond · protein-protein

Compared structures

4JEN · Structure of Clostridium botulinum CMP N-glycosidase, BcmB · 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 A7FS24
Elsewhere: RCSB PDB 4JEN · PDBe 4JEN · UniProt A7FS24

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