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Histidine kinase domain from erythrobacter litoralis EL346 blue-light activated histidine kinase

Analyse Histidine kinase domain from erythrobacter litoralis EL346 blue-light activated… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4R39
Type: protein
Length: 843 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Blue-light-activated histidine kinase 2
EC: 2.7.13.3
UniProt: Q2NB77
Ligands: ANP, MG
Pockets: 9 · best druggability 0.79

Structure

x-ray diffraction · 3 distinct chains · 51% helix, 20% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, D	Blue-light-activated histidine kinase 2 (EC 2.7.13.3)	protein	217	50% helix, 18% strand	Q2NB77
B	Blue-light-activated histidine kinase 2 (EC 2.7.13.3)	protein	205	51% helix, 21% strand	Q2NB77
C	Blue-light-activated histidine kinase 2 (EC 2.7.13.3)	protein	204	53% helix, 20% strand	Q2NB77

Ligands and binding sites

ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · 4 copies · chains A, B, C, D
MG · Magnesium ion · metal · 4 copies · chains A, B, C, D

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	174	0.79	0.95	44	empty
2	419	0.64	0.78	61	empty
3	414	0.63	0.77	56	empty
4	164	0.58	0.82	30	MG, ANP
5	176	0.58	0.82	26	MG, ANP

Interfaces

6 interfaces between chains.

C–D · 1105 Å² buried · 26 hydrogen bonds · protein-protein
A–B · 1091 Å² buried · 26 hydrogen bonds · protein-protein
B–D · 1016 Å² buried · 19 hydrogen bonds · protein-protein
A–C · 975 Å² buried · 18 hydrogen bonds · protein-protein
A–D · 196 Å² buried · 3 hydrogen bonds · protein-protein

Compared structures

4R39 · Histidine kinase domain from Erythrobacter litoralis EL346 blue-light activated histidine… · the same entry in another collection · chain A against A, TM-score 1.00
Q2NB77 · AlphaFold monomer V2.0 prediction for blue-light-activated histidine kinase 2 (Q2NB77) · a predicted model of the same protein · chain C against A, TM-score 0.85

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 Q2NB77
Elsewhere: RCSB PDB 4R39 · PDBe 4R39 · UniProt Q2NB77

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