MolNFT v1 · #116861 · protein

The crystal structure of bacillus subtilis ypgq

5DQV · Uncharacterized protein: “The crystal structure of bacillus subtilis ypgq”. X-ray diffraction, 1 ligand (NI), 3 pockets (best druggability 0.61). MolNFT v1 #116861 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5DQV
Type: protein
Length: 374 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 0.61

Structure

x-ray diffraction · 2 distinct chains · 71% 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	186	70% 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	419	0.61	0.76	40	empty
2	444	0.60	0.75	43	NI
3	80	0.39	0.77	18	empty

Interfaces

1 interface between chains.

A–B · 1173 Å² buried · 5 hydrogen bonds · protein-protein

Compared structures

5DQV · The crystal structure of Bacillus subtilis 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 5DQV · PDBe 5DQV · UniProt A0A0D5CVW2

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