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Crystal structure of polyphosphate kinase from meiothermus ruber bound to ADP and ppi

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

PDB: 5MAQ
Type: protein
Length: 1,032 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: POLYPHOSPHATE:AMP phosphotransferase
UniProt: A0A0S7ASE9
Ligands: ADP, PPV, MG
Pockets: 8 · best druggability 0.78

Structure

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

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	POLYPHOSPHATE:AMP phosphotransferase	protein	257	51% helix, 13% strand	A0A0S7ASE9
B	POLYPHOSPHATE:AMP phosphotransferase	protein	256	50% helix, 13% strand	A0A0S7ASE9
C	POLYPHOSPHATE:AMP phosphotransferase	protein	258	47% helix, 13% strand	A0A0S7ASE9
D	POLYPHOSPHATE:AMP phosphotransferase	protein	261	50% helix, 13% strand	A0A0S7ASE9

Ligands and binding sites

ADP · Adenosine-5'-diphosphate · ligand · 4 copies · chains A, B, C, D
PPV · Pyrophosphate · ligand · 4 copies · chains A, B, C, D
MG · Magnesium ion · metal · 4 copies · chains A, B, D

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

Pockets

8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	559	0.78	0.85	76	empty
2	295	0.68	0.83	45	ADP, PPV
3	304	0.64	0.81	35	PPV, MG
4	61	0.43	0.82	19	ADP
5	50	0.42	0.83	15	empty

Interfaces

6 interfaces between chains.

A–B · 1385 Å² buried · 25 hydrogen bonds · protein-protein
C–D · 1377 Å² buried · 24 hydrogen bonds · protein-protein
A–D · 1342 Å² buried · 9 hydrogen bonds · protein-protein
B–C · 1046 Å² buried · 3 hydrogen bonds · protein-protein
B–D · 136 Å² buried · 2 hydrogen bonds · protein-protein

Compared structures

5MAQ · Crystal Structure of Polyphosphate Kinase from Meiothermus ruber bound to ADP and PPi · 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 5MAQ · PDBe 5MAQ · UniProt A0A0S7ASE9

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