Research workbench

Crystal structure of chey D13K Y106W alone and in complex with a flim peptide

Analyse Crystal structure of chey D13K Y106W alone and in complex with a flim peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1U8T
Type: protein
Length: 535 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Chemotaxis protein chey; Flagellar motor switch protein flim
UniProt: P06143, P06974
Ligands: MSE, SO4
Pockets: 2 · best druggability 0.82

Structure

x-ray diffraction · 3 distinct chains · 45% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Chemotaxis protein chey	protein	125	43% helix, 18% strand	P06143
B, C, D	Chemotaxis protein chey	protein	128	45% helix, 17% strand	P06143
E, F	Flagellar motor switch protein flim	protein	13	62% helix, 8% strand	P06974

Ligands and binding sites

MSE · Selenomethionine · ligand · chains A
SO4 · Sulfate ion · ion · 4 copies · chains C, D

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1009	0.82	0.83	102	SO4
2	162	0.43	0.75	42	empty

Interfaces

9 interfaces between chains.

A–C · 562 Å² buried · 5 hydrogen bonds · protein-protein
B–D · 546 Å² buried · 6 hydrogen bonds · protein-protein
B–F · 527 Å² buried · 9 hydrogen bonds · protein-protein
A–E · 511 Å² buried · 10 hydrogen bonds · protein-protein
A–B · 309 Å² buried · 4 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 23 modified (engineered).

Compared structures

1U8T · Crystal structure of CheY D13K Y106W alone and in complex with a FliM peptide · the same entry in another collection · chain F against F, TM-score 1.00
P06974 · AlphaFold monomer V2.0 prediction for flagellar motor switch protein flim (P06974) · a predicted model of the same protein · chain F against A, TM-score 0.55

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 P06143
Every structure of UniProt P06974
Elsewhere: RCSB PDB 1U8T · PDBe 1U8T · UniProt P06143 · UniProt P06974

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