MolNFT v1 · #128381 · protein

Polysaccharide lyase BACCELL_00875

5NOK: “Polysaccharide lyase BACCELL_00875”. X-ray diffraction, 14 pockets (best druggability 0.70). MolNFT v1 #128381 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5NOK
Type: protein
Length: 1,337 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: BACCELL_00875
UniProt: E2N9D0
Pockets: 14 · best druggability 0.70

Structure

x-ray diffraction · 2 distinct chains · 33% helix, 28% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	BACCELL_00875	protein	668	33% helix, 28% strand	E2N9D0
B	BACCELL_00875	protein	669	33% helix, 28% strand	E2N9D0

Ligands and binding sites

MES · 2-(N-morpholino)-ethanesulfonic acid · additive · chains B

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

Pockets

14 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	219	0.70	0.86	32	empty
2	451	0.67	0.79	57	empty
3	467	0.66	0.78	52	empty
4	97	0.64	0.90	25	MES
5	339	0.62	0.79	31	empty

Interfaces

1 interface between chains.

A–B · 1452 Å² buried · 14 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 30 modified (engineered).

Compared structures

5NOK · Polysaccharide Lyase BACCELL_00875 · 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 E2N9D0
Elsewhere: RCSB PDB 5NOK · PDBe 5NOK · UniProt E2N9D0

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