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Sporosarcina pasteurii urease inhibited by silver

Analyse Sporosarcina pasteurii urease inhibited by silver in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6G48
Type: protein
Length: 792 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Urease subunit gamma; Urease subunit beta; Urease subunit alpha
EC: 3.5.1.5
UniProt: A0A0H3YGY5, P41021, A0A0H3YL32
Ligands: NI, AG, SO4, OH
Pockets: 4 · best druggability 0.71

Structure

x-ray diffraction · 3 distinct chains · 30% helix, 24% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Urease subunit gamma (EC 3.5.1.5)	protein	100	56% helix, 18% strand	A0A0H3YGY5
B	Urease subunit beta (EC 3.5.1.5)	protein	122	15% helix, 31% strand	P41021
C	Urease subunit alpha	protein	570	29% helix, 23% strand	A0A0H3YL32

Ligands and binding sites

NI · Nickel (II) ion · metal · 2 copies · chains C
AG · Silver ion · metal · 2 copies · chains C
SO4 · Sulfate ion · ion · 6 copies · chains A, C, B
OH · Hydroxide ion · ion · chains C
EDO · 1,2-ethanediol · additive · 10 copies · chains A, C, B

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

Pockets

4 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	692	0.71	0.78	60	EDO
2	57	0.48	0.86	17	NI, OH, EDO, SO4
3	121	0.40	0.76	22	empty
4	115	0.39	0.75	19	EDO

Interfaces

3 interfaces between chains.

B–C · 1866 Å² buried · 32 hydrogen bonds · protein-protein
A–C · 950 Å² buried · 14 hydrogen bonds · protein-protein
A–B · 219 Å² buried · 5 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 modified (carboxylation).

Compared structures

6G48 · Sporosarcina pasteurii urease inhibited by silver · the same entry in another collection · chain A against A, TM-score 1.00
P41021 · AlphaFold monomer V2.0 prediction for urease subunit beta (P41021) · a predicted model of the same protein · chain B against A, TM-score 0.98

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 A0A0H3YGY5
Every structure of UniProt P41021
Every structure of UniProt A0A0H3YL32
Elsewhere: RCSB PDB 6G48 · PDBe 6G48 · UniProt A0A0H3YGY5 · UniProt P41021 · UniProt A0A0H3YL32

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