MolNFT v1 · #167952 · protein

Putative kojibiose phosphorylase from human microbiome

6W0P: “Putative kojibiose phosphorylase from human microbiome”. X-ray diffraction, 20 pockets (best druggability 0.79). MolNFT v1 #167952 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6W0P
Type: protein
Length: 2,899 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Kojibiose phosphorylase
Pockets: 20 · best druggability 0.79

Structure

x-ray diffraction · 4 distinct chains · 35% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Kojibiose phosphorylase	protein	752	33% helix, 26% strand	—
B	Kojibiose phosphorylase	protein	751	33% helix, 26% strand	—
C	Kojibiose phosphorylase	protein	719	35% helix, 21% strand	—
D	Kojibiose phosphorylase	protein	677	37% helix, 19% strand	—

Pockets

20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1024	0.79	0.80	93	empty
2	913	0.76	0.79	51	empty
3	168	0.75	0.92	37	empty
4	969	0.75	0.78	76	empty
5	969	0.75	0.78	88	empty

Interfaces

3 interfaces between chains.

A–B · 1926 Å² buried · 44 hydrogen bonds · protein-protein
C–D · 1915 Å² buried · 42 hydrogen bonds · protein-protein
B–D · 255 Å² buried · 6 hydrogen bonds · protein-protein

Compared structures

6W0P · Putative kojibiose phosphorylase from human microbiome · the same entry in another collection · chain B against B, 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
Elsewhere: RCSB PDB 6W0P · PDBe 6W0P

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