Research workbench

Gphf gnat-like decarboxylase

Analyse Gphf gnat-like decarboxylase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6MFC
Type: protein
Length: 390 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Gphf
UniProt: U6BSB2
Pockets: 5 · best druggability 0.71

Structure

x-ray diffraction · 1 distinct chain · 38% helix, 25% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
B, A	Gphf	protein	195	38% helix, 25% strand	U6BSB2

Ligands and binding sites

GOL · Glycerol · additive · 3 copies · chains B, A
1PE · Pentaethylene glycol · additive · 2 copies · chains B, A

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

Pockets

5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	422	0.71	0.82	49	GOL, 1PE
2	351	0.71	0.83	45	GOL, 1PE
3	155	0.46	0.76	19	empty
4	81	0.33	0.75	17	empty
5	56	0.33	0.77	15	empty

Interfaces

1 interface between chains.

B–A · 547 Å² buried · 6 hydrogen bonds · protein-protein

Compared structures

6MFC · GphF GNAT-like decarboxylase · 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
Every structure of UniProt U6BSB2
Elsewhere: RCSB PDB 6MFC · PDBe 6MFC · UniProt U6BSB2

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