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Crystal structure of the extracellular domain of the putative histidine kinase MMHK1S-Z3

Analyse Crystal structure of the extracellular domain of the putative histidine kinase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3LIB
Type: protein
Length: 2,699 residues
Chains: 10
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Hypothetical sensory transduction histidine kinase
UniProt: Q8PSW1
Ligands: K
Pockets: 20 · best druggability 0.79

Structure

x-ray diffraction · 4 distinct chains · 34% helix, 27% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, D, F, I, J	Hypothetical sensory transduction histidine kinase	protein	271	34% helix, 27% strand	Q8PSW1
C, E	Hypothetical sensory transduction histidine kinase	protein	268	35% helix, 27% strand	Q8PSW1
G	Hypothetical sensory transduction histidine kinase	protein	270	32% helix, 28% strand	Q8PSW1
H	Hypothetical sensory transduction histidine kinase	protein	267	34% helix, 27% strand	Q8PSW1

Ligands and binding sites

K · Potassium ion · metal · 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

20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1193	0.79	0.81	129	empty
2	340	0.76	0.87	51	empty
3	350	0.75	0.86	58	empty
4	253	0.70	0.85	35	empty
5	211	0.68	0.85	33	empty

Interfaces

19 interfaces between chains.

A–B · 1517 Å² buried · 21 hydrogen bonds · protein-protein
G–H · 1516 Å² buried · 28 hydrogen bonds · protein-protein
C–D · 1512 Å² buried · 25 hydrogen bonds · protein-protein
I–J · 1503 Å² buried · 23 hydrogen bonds · protein-protein
E–F · 1493 Å² buried · 26 hydrogen bonds · protein-protein

Compared structures

3LIB · Crystal Structure of the extracellular domain of the putative histidine kinase mmHK1S-Z3 · the same entry in another collection · chain A 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 Q8PSW1
Elsewhere: RCSB PDB 3LIB · PDBe 3LIB · UniProt Q8PSW1

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