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Crystal structure of C-terminal domain of SMU_1151C from streptococcus mutans

Analyse Crystal structure of C-terminal domain of SMU_1151C from streptococcus mutans in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2QKP
Type: protein
Length: 548 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Uncharacterized protein
UniProt: Q8DU08
Pockets: 8 · best druggability 0.66

Structure

x-ray diffraction · 3 distinct chains · 29% helix, 35% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Uncharacterized protein	protein	138	30% helix, 35% strand	Q8DU08
B, C	Uncharacterized protein	protein	138	27% helix, 34% strand	Q8DU08
D	Uncharacterized protein	protein	134	29% helix, 35% strand	Q8DU08

Ligands and binding sites

EDO · 1,2-ethanediol · additive · 2 copies · chains B, C
GOL · Glycerol · additive · chains D

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

Pockets

8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	455	0.66	0.78	44	EDO
2	360	0.61	0.77	37	GOL
3	148	0.54	0.80	23	empty
4	211	0.54	0.78	29	EDO
5	224	0.52	0.76	29	empty

Interfaces

3 interfaces between chains.

A–B · 2248 Å² buried · 31 hydrogen bonds · protein-protein
C–D · 2180 Å² buried · 25 hydrogen bonds · protein-protein
A–C · 498 Å² buried · 11 hydrogen bonds · protein-protein

Compared structures

2QKP · Crystal structure of C-terminal domain of SMU_1151c from Streptococcus mutans · 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 Q8DU08
Elsewhere: RCSB PDB 2QKP · PDBe 2QKP · UniProt Q8DU08

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