MolNFT v1 · #125555 · protein

Structure of polyphosphate kinase from meiothermus ruber apo-form

5LC9 · POLYPHOSPHATE:AMP phosphotransferase: “Structure of polyphosphate kinase from meiothermus ruber apo-form”. X-ray diffraction, 2 ligands (PO4, SO4), 14 pockets (best druggability 0.80). MolNFT v1 #125555 on GenesisL1: 3D structure…

PDB: 5LC9
Type: protein
Length: 1,027 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: POLYPHOSPHATE:AMP phosphotransferase
UniProt: A0A0S7ASE9
Ligands: PO4, SO4
Pockets: 14 · best druggability 0.80

Structure

x-ray diffraction · 3 distinct chains · 50% helix, 13% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	POLYPHOSPHATE:AMP phosphotransferase	protein	256	50% helix, 13% strand	A0A0S7ASE9
B	POLYPHOSPHATE:AMP phosphotransferase	protein	258	51% helix, 13% strand	A0A0S7ASE9
D	POLYPHOSPHATE:AMP phosphotransferase	protein	257	50% helix, 13% strand	A0A0S7ASE9

Ligands and binding sites

PO4 · Phosphate ion · ion · 4 copies · chains A, B, C, D
SO4 · Sulfate ion · ion · 4 copies · chains A, B, C, 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, 8 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	642	0.80	0.85	84	empty
2	456	0.72	0.82	50	PO4, SO4
3	201	0.64	0.84	34	PO4, SO4
4	101	0.60	0.87	26	PO4, SO4
5	74	0.53	0.86	22	empty

Interfaces

6 interfaces between chains.

A–B · 1299 Å² buried · 29 hydrogen bonds · protein-protein
C–D · 1292 Å² buried · 27 hydrogen bonds · protein-protein
B–C · 1099 Å² buried · 6 hydrogen bonds · protein-protein
A–D · 1083 Å² buried · 10 hydrogen bonds · protein-protein
A–C · 137 Å² buried · 2 hydrogen bonds · protein-protein

Compared structures

5LC9 · Structure of Polyphosphate Kinase from Meiothermus ruber Apo-form · the same entry in another collection · chain C against C, 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 A0A0S7ASE9
Elsewhere: RCSB PDB 5LC9 · PDBe 5LC9 · UniProt A0A0S7ASE9

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