MolNFT v1 · #128974 · protein

Structure of polyphosphate kinase from meiothermus ruber N121D

5O6K · POLYPHOSPHATE:AMP phosphotransferase: “Structure of polyphosphate kinase from meiothermus ruber N121D”. X-ray diffraction, 2 ligands (DPO, PO4), 11 pockets (best druggability 0.81). MolNFT v1 #128974 on GenesisL1: 3D structure…

PDB: 5O6K
Type: protein
Length: 1,034 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: POLYPHOSPHATE:AMP phosphotransferase
UniProt: A0A0S7ASE9
Ligands: DPO, PO4
Pockets: 11 · best druggability 0.81

Structure

x-ray diffraction · 4 distinct chains · 50% helix, 13% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	POLYPHOSPHATE:AMP phosphotransferase	protein	258	51% helix, 13% strand	A0A0S7ASE9
B	POLYPHOSPHATE:AMP phosphotransferase	protein	256	50% helix, 13% strand	A0A0S7ASE9
C	POLYPHOSPHATE:AMP phosphotransferase	protein	260	49% helix, 13% strand	A0A0S7ASE9
D	POLYPHOSPHATE:AMP phosphotransferase	protein	260	48% helix, 13% strand	A0A0S7ASE9

Ligands and binding sites

DPO · Diphosphate · ligand · 2 copies · chains B
PO4 · Phosphate ion · ion · 10 copies · chains A, B, C, D

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

Pockets

11 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	955	0.81	0.83	102	empty
2	619	0.70	0.78	71	PO4
3	387	0.69	0.82	42	PO4
4	291	0.64	0.81	40	PO4
5	230	0.63	0.83	33	PO4

Interfaces

6 interfaces between chains.

A–D · 1496 Å² buried · 8 hydrogen bonds · protein-protein
C–D · 1330 Å² buried · 27 hydrogen bonds · protein-protein
A–B · 1315 Å² buried · 23 hydrogen bonds · protein-protein
B–C · 1302 Å² buried · 4 hydrogen bonds · protein-protein
B–D · 91 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

5O6K · Structure of Polyphosphate Kinase from Meiothermus ruber N121D · 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
Every structure of UniProt A0A0S7ASE9
Elsewhere: RCSB PDB 5O6K · PDBe 5O6K · UniProt A0A0S7ASE9

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