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The crystal structure of bacillus subtilis semet-ypgq

Analyse The crystal structure of bacillus subtilis semet-ypgq in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5IHY
Type: protein
Length: 381 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Uncharacterized protein
UniProt: A0A0D5CVW2
Ligands: NI
Pockets: 3 · best druggability 0.66

Structure

x-ray diffraction · 2 distinct chains · 72% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Uncharacterized protein	protein	188	71% helix, 0% strand	A0A0D5CVW2
B	Uncharacterized protein	protein	193	73% helix, 0% strand	A0A0D5CVW2

Ligands and binding sites

NI · Nickel (II) ion · metal · 2 copies · chains A, 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, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	602	0.66	0.76	59	NI
2	440	0.62	0.76	44	NI
3	80	0.39	0.77	18	empty

Interfaces

1 interface between chains.

A–B · 1285 Å² buried · 8 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 11 modified (engineered).

Compared structures

5IHY · The crystal structure of Bacillus subtilis SeMet-YpgQ · 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 A0A0D5CVW2
Elsewhere: RCSB PDB 5IHY · PDBe 5IHY · UniProt A0A0D5CVW2

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