MolNFT v1 · #27235 · protein

Crystal structure of escherichia COLI polyphosphate kinase

1XDO: “Crystal structure of escherichia COLI polyphosphate kinase”. X-ray diffraction, 14 pockets (best druggability 0.81). MolNFT v1 #27235 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1XDO
Type: protein
Length: 1,374 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Polyphosphate kinase
EC: 2.7.4.1
UniProt: P0A7B1
Pockets: 14 · best druggability 0.81

Structure

x-ray diffraction · 1 distinct chain · 39% helix, 21% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Polyphosphate kinase (EC 2.7.4.1)	protein	687	39% helix, 21% strand	P0A7B1

Pockets

14 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	986	0.81	0.83	90	empty
2	1000	0.81	0.82	95	empty
3	635	0.75	0.81	53	empty
4	640	0.75	0.81	61	empty
5	540	0.73	0.81	64	empty

Interfaces

1 interface between chains.

A–B · 1720 Å² buried · 22 hydrogen bonds · protein-protein

Compared structures

1XDO · Crystal Structure of Escherichia coli Polyphosphate Kinase · the same entry in another collection · chain A against A, TM-score 1.00
P0A7B1 · AlphaFold monomer V2.0 prediction for polyphosphate kinase (P0A7B1) · a predicted model of the same protein · chain A against A, TM-score 0.94

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 P0A7B1
Elsewhere: RCSB PDB 1XDO · PDBe 1XDO · UniProt P0A7B1

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