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Crystal structure of polyphosphate kinase from meiothermus ruber bound to ATP

Analyse Crystal structure of polyphosphate kinase from meiothermus ruber bound to ATP in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5LD1
Type: protein
Length: 1,039 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: POLYPHOSPHATE:AMP phosphotransferase
UniProt: A0A0S7ASE9
Ligands: ATP, MG, SO4
Pockets: 9 · best druggability 0.76

Structure

x-ray diffraction · 3 distinct chains · 52% helix, 13% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	POLYPHOSPHATE:AMP phosphotransferase	protein	257	53% helix, 13% strand	A0A0S7ASE9
B	POLYPHOSPHATE:AMP phosphotransferase	protein	260	52% helix, 13% strand	A0A0S7ASE9
C, D	POLYPHOSPHATE:AMP phosphotransferase	protein	261	51% helix, 13% strand	A0A0S7ASE9

Ligands and binding sites

ATP · Adenosine-5'-triphosphate · ligand · 8 copies · chains A, D, B, C
MG · Magnesium ion · metal · 7 copies · chains A, B, D, C
SO4 · Sulfate ion · ion · 4 copies · chains A, B, C, D
GOL · Glycerol · additive · 2 copies · chains B, C

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

Pockets

9 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	489	0.76	0.84	70	ATP, MG, GOL
2	582	0.75	0.82	67	ATP, MG
3	534	0.75	0.83	64	ATP, MG
4	217	0.63	0.83	39	empty
5	220	0.62	0.82	28	ATP, GOL

Interfaces

6 interfaces between chains.

B–C · 1622 Å² buried · 16 hydrogen bonds · protein-protein
A–D · 1327 Å² buried · 16 hydrogen bonds · protein-protein
A–B · 1321 Å² buried · 29 hydrogen bonds · protein-protein
C–D · 1302 Å² buried · 28 hydrogen bonds · protein-protein
A–C · 35 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

5LD1 · Crystal Structure of Polyphosphate Kinase from Meiothermus ruber bound to ATP · 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 5LD1 · PDBe 5LD1 · UniProt A0A0S7ASE9

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