MolNFT v1 · #139389 · protein

Crystal structure of the complex of the peptidase domain of streptococcus mutans coma with a small molecule inhibitor.

5XE9 · Putative ABC transporter, ATP-binding protein coma: “Crystal structure of the complex of the peptidase domain of streptococcus mutans coma with a small molecule…”. X-ray diffraction, 1 ligand (6CH), 3 pockets (best druggability…

PDB: 5XE9
Type: protein
Length: 258 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Putative ABC transporter, ATP-binding protein coma
UniProt: Q8DW05
Ligands: 6CH
Pockets: 3 · best druggability 0.49

Structure

x-ray diffraction · 2 distinct chains · 29% helix, 36% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Putative ABC transporter, ATP-binding protein coma	protein	136	33% helix, 35% strand	Q8DW05
B	Putative ABC transporter, ATP-binding protein coma	protein	122	25% helix, 36% strand	Q8DW05

Ligands and binding sites

6CH · [(1~{S},2~{R},4~{S},5~{R})-5-[5-(4-methoxyphenyl)-2-methyl-pyrazol-3-yl]-1-azabicyclo[2.2.2]octan-2-yl]methyl ~{N}-propylcarbamate · ligand · chains B

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

Pockets

3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	141	0.49	0.78	18	empty
2	74	0.41	0.80	15	empty
3	61	0.39	0.80	14	empty

Interfaces

1 interface between chains.

A–B · 943 Å² buried · 10 hydrogen bonds · protein-protein

Compared structures

5XE9 · Crystal Structure of the Complex of the Peptidase Domain of Streptococcus mutans ComA… · 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 Q8DW05
Elsewhere: RCSB PDB 5XE9 · PDBe 5XE9 · UniProt Q8DW05

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