MolNFT v1 · #152655 · protein

Crystal structure of porphyromonas gingivalis acetate kinase

6IOY: “Crystal structure of porphyromonas gingivalis acetate kinase”. X-ray diffraction, 1 ligand (SO4), 14 pockets (best druggability 0.84). MolNFT v1 #152655 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6IOY
Type: protein
Length: 1,596 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Acetate kinase
EC: 2.7.2.1
UniProt: B2RK02
Ligands: SO4
Pockets: 14 · best druggability 0.84

Structure

x-ray diffraction · 3 distinct chains · 43% helix, 21% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Acetate kinase (EC 2.7.2.1)	protein	399	43% helix, 21% strand	B2RK02
B	Acetate kinase (EC 2.7.2.1)	protein	401	43% helix, 20% strand	B2RK02
C, D	Acetate kinase (EC 2.7.2.1)	protein	398	42% helix, 21% strand	B2RK02

Ligands and binding sites

SO4 · Sulfate ion · ion · 5 copies · chains A, B, C, D
MPD · (4S)-2-methyl-2,4-pentanediol · additive · 2 copies · chains A, B, D

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

Pockets

14 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	216	0.84	0.97	51	empty
2	192	0.82	0.97	41	empty
3	775	0.76	0.81	63	SO4
4	772	0.71	0.77	74	empty
5	601	0.66	0.76	63	empty

Interfaces

3 interfaces between chains.

C–D · 3118 Å² buried · 27 hydrogen bonds · protein-protein
A–B · 3068 Å² buried · 27 hydrogen bonds · protein-protein
A–C · 91 Å² buried · 1 hydrogen bond · protein-protein

Compared structures

6IOY · Crystal structure of Porphyromonas gingivalis acetate kinase · the same entry in another collection · chain D against D, TM-score 1.00
B2RK02 · AlphaFold monomer V2.0 prediction for acetate kinase (B2RK02) · a predicted model of the same protein · chain B against A, TM-score 0.98

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 B2RK02
Elsewhere: RCSB PDB 6IOY · PDBe 6IOY · UniProt B2RK02

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.