MolNFT v1 · #144931 · protein

Last common ancestor of ADP-dependent phosphofructokinases from methanosarcinales

6C8Z: “Last common ancestor of ADP-dependent phosphofructokinases from methanosarcinales”. X-ray diffraction, 3 ligands (ADP, NI, MG), 4 pockets (best druggability 0.66). MolNFT v1 #144931 on GenesisL1: 3D structure, binding sites and…

PDB: 6C8Z
Type: protein
Length: 488 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: ADP-dependent phosphofructokinase
EC: 2.7.1.146
Ligands: ADP, NI, MG
Pockets: 4 · best druggability 0.66

Structure

x-ray diffraction · 1 distinct chain · 46% helix, 20% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	ADP-dependent phosphofructokinase (EC 2.7.1.146)	protein	488	46% helix, 20% strand	—

Ligands and binding sites

ADP · Adenosine-5'-diphosphate · ligand · chains A
NI · Nickel (II) ion · metal · 3 copies · chains A
MG · Magnesium ion · metal · chains A

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	601	0.66	0.76	61	ADP, MG
2	121	0.45	0.77	19	empty
3	59	0.34	0.78	16	empty
4	53	0.29	0.75	15	empty

Compared structures

6C8Z · Last common ancestor of ADP-dependent phosphofructokinases from Methanosarcinales · 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
Elsewhere: RCSB PDB 6C8Z · PDBe 6C8Z

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