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Crystal structure of E.COLI dha kinase dhak (H56N)

Analyse Crystal structure of E.COLI dha kinase dhak (H56N) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3PNO
Type: protein
Length: 1,350 residues
Chains: 4
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: 15 · best druggability 0.83

Structure

x-ray diffraction · 2 distinct chains · 32% helix, 31% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Pts-dependent dihydroxyacetone kinase, dihydroxyacetone- binding subunit dhak (EC 2.7.-.-)	protein	336	32% helix, 32% strand	P76015
C, D	Pts-dependent dihydroxyacetone kinase, dihydroxyacetone- binding subunit dhak (EC 2.7.-.-)	protein	339	32% helix, 31% strand	P76015

Pockets

15 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	858	0.83	0.85	83	empty
2	1092	0.82	0.83	105	empty
3	71	0.71	0.96	21	empty
4	182	0.49	0.77	33	empty
5	102	0.46	0.80	22	empty

Interfaces

3 interfaces between chains.

C–D · 1334 Å² buried · 10 hydrogen bonds · protein-protein
A–B · 1317 Å² buried · 10 hydrogen bonds · protein-protein
A–C · 528 Å² buried · 3 hydrogen bonds · protein-protein

Compared structures

3PNO · Crystal Structure of E.coli Dha kinase DhaK (H56N) · the same entry in another collection · chain D against D, 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 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 P76015
Elsewhere: RCSB PDB 3PNO · PDBe 3PNO · UniProt P76015

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