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Crystal structure of E.COLI dha kinase dhak

Analyse Crystal structure of E.COLI dha kinase dhak in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3PNK
Type: protein
Length: 708 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Pts-dependent dihydroxyacetone kinase, dihydroxyacetone- binding subunit dhak
EC: 2.7.-.-
UniProt: P76015
Pockets: 8 · best druggability 0.83

Structure

x-ray diffraction · 1 distinct chain · 31% helix, 30% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Pts-dependent dihydroxyacetone kinase, dihydroxyacetone- binding subunit dhak (EC 2.7.-.-)	protein	354	31% helix, 30% strand	P76015

Ligands and binding sites

GOL · Glycerol · additive · 2 copies · chains A, B

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

Pockets

8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1084	0.83	0.84	100	empty
2	414	0.60	0.76	36	empty
3	74	0.34	0.75	16	empty
4	75	0.33	0.75	23	empty
5	67	0.31	0.75	17	empty

Interfaces

1 interface between chains.

A–B · 2010 Å² buried · 30 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 covalent (additive adduct).

Compared structures

3PNK · Crystal Structure of E.coli Dha kinase DhaK · the same entry in another collection · chain A against A, TM-score 1.00
P76015 · AlphaFold monomer V2.0 prediction for pep-dependent dihydroxyacetone kinase… · a predicted model of the same protein · chain B against A, TM-score 0.98

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 P76015
Elsewhere: RCSB PDB 3PNK · PDBe 3PNK · UniProt P76015

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