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Sensor kinase cita binding domain

Analyse Sensor kinase cita binding domain in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1P0Z
Type: protein
Length: 1,310 residues
Chains: 10
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Sensor kinase cita
EC: 2.7.13.3
UniProt: P52687
Ligands: MO7, OMO, NA
Pockets: 18 · best druggability 0.73

Structure

x-ray diffraction · 1 distinct chain · 37% helix, 30% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F, G, H, I, J	Sensor kinase cita (EC 2.7.13.3)	protein	131	37% helix, 30% strand	P52687

Ligands and binding sites

MO7 · bis(mu4-oxo)-bis(mu3-oxo)-octakis(mu2-oxo)-dodecaoxo-heptamolybdenum (VI) · ligand · 10 copies · chains A, B, C, D, E, G, F, J, H, I
OMO · Mo(vi)(=o)(oh)2 cluster · ligand · 10 copies · chains A, B, C, D, E, F, G, H, I, J
NA · Sodium ion · metal · 10 copies · chains A, B, C, D, E, F, G, H, I, J
FLC · Citrate anion · additive · 10 copies · chains A, B, C, D, E, F, G, H, I, J

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	750	0.73	0.79	68	MO7
2	324	0.71	0.84	30	empty
3	77	0.60	0.90	21	FLC, OMO
4	118	0.59	0.86	24	FLC, OMO
5	73	0.59	0.89	18	FLC, OMO

Interfaces

7 interfaces between chains.

E–G · 910 Å² buried · 11 hydrogen bonds · protein-protein
G–J · 730 Å² buried · 13 hydrogen bonds · protein-protein
B–D · 374 Å² buried · 3 hydrogen bonds · protein-protein
B–E · 347 Å² buried · 2 hydrogen bonds · protein-protein
A–G · 157 Å² buried · 1 hydrogen bond · protein-protein

Compared structures

1P0Z · Sensor Kinase CitA binding domain · the same entry in another collection · chain J against J, TM-score 1.00
P52687 · AlphaFold monomer V2.0 prediction for sensor histidine kinase cita (P52687) · a predicted model of the same protein · chain H against A, TM-score 0.96

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 P52687
Elsewhere: RCSB PDB 1P0Z · PDBe 1P0Z · UniProt P52687

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