MolNFT v1 · #156786 · protein

Gphf gnat-like decarboxylase in complex with isobutyryl-CoA

6MFD: “Gphf gnat-like decarboxylase in complex with isobutyryl-CoA”. X-ray diffraction, 1 ligand (CO6), 5 pockets (best druggability 0.72). MolNFT v1 #156786 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6MFD
Type: protein
Length: 390 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Gphf
UniProt: U6BSB2
Ligands: CO6
Pockets: 5 · best druggability 0.72

Structure

x-ray diffraction · 1 distinct chain · 37% helix, 26% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
B, A	Gphf	protein	195	37% helix, 26% strand	U6BSB2

Ligands and binding sites

CO6 · Isobutyryl-coenzyme A · ligand · 2 copies · chains B, A
GOL · Glycerol · additive · 2 copies · chains A
ACT · Acetate ion · additive · 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	440	0.72	0.82	51	CO6, GOL
2	353	0.70	0.83	38	CO6
3	78	0.45	0.82	17	ACT
4	75	0.34	0.76	17	empty
5	59	0.33	0.78	14	empty

Interfaces

1 interface between chains.

B–A · 538 Å² buried · 6 hydrogen bonds · protein-protein

Compared structures

6MFD · GphF GNAT-like decarboxylase in complex with isobutyryl-CoA · 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 6MFD · PDBe 6MFD · UniProt U6BSB2

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