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Crystal structure of the E.COLI DHAR(N)-dhal complex

Analyse Crystal structure of the E.COLI DHAR(N)-dhal complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4LRZ
Type: protein
Length: 2,017 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Pts-dependent dihydroxyacetone kinase, ADP-binding subunit dhal; Pts-dependent…
EC: 2.7.-.-
UniProt: P76014, P76016
Ligands: ADP, MG
Pockets: 12 · best druggability 0.86

Structure

x-ray diffraction · 3 distinct chains · 52% helix, 21% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Pts-dependent dihydroxyacetone kinase, ADP-binding subunit dhal (EC 2.7.-.-)	protein	211	75% helix, 3% strand	P76014
E, F, G	Pts-dependent dihydroxyacetone kinase operon regulatory protein	protein	294	43% helix, 28% strand	P76016
H	Pts-dependent dihydroxyacetone kinase operon regulatory protein	protein	291	44% helix, 27% strand	P76016

Ligands and binding sites

ADP · Adenosine-5'-diphosphate · ligand · 4 copies · chains A, F, B, H, C, G, D, E
MG · Magnesium ion · metal · 8 copies · chains A, B, C, D

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

Pockets

12 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1123	0.86	0.87	127	ADP, MG
2	845	0.84	0.86	96	ADP, MG
3	831	0.84	0.86	88	ADP, MG
4	884	0.83	0.85	100	ADP, MG
5	754	0.75	0.80	87	empty

Interfaces

11 interfaces between chains.

E–G · 2485 Å² buried · 21 hydrogen bonds · protein-protein
F–H · 2471 Å² buried · 21 hydrogen bonds · protein-protein
C–G · 1073 Å² buried · 10 hydrogen bonds · protein-protein
D–E · 1061 Å² buried · 12 hydrogen bonds · protein-protein
B–H · 1052 Å² buried · 11 hydrogen bonds · protein-protein

Compared structures

4LRZ · Crystal Structure of the E.coli DhaR(N)-DhaL complex · the same entry in another collection · chain H against H, TM-score 1.00
P76014 · AlphaFold monomer V2.0 prediction for pep-dependent dihydroxyacetone kinase, ADP-binding… · a predicted model of the same protein · chain C against A, TM-score 0.99

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 P76014
Every structure of UniProt P76016
Elsewhere: RCSB PDB 4LRZ · PDBe 4LRZ · UniProt P76014 · UniProt P76016

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