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B. subtilis prophage dutpase yoss in complex with dump

Analyse B. subtilis prophage dutpase yoss in complex with dump in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4AO5
Type: protein
Length: 771 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: SPBC2 prophage-derived deoxyuridine 5'-triphosphate nucleo tidohydrolase yoss
EC: 3.6.1.23
UniProt: O34919
Ligands: UMP, NA
Pockets: 9 · best druggability 0.72

Structure

x-ray diffraction · 2 distinct chains · 4% helix, 48% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C, F	SPBC2 prophage-derived deoxyuridine 5'-triphosphate nucleo tidohydrolase yoss (EC 3.6.1.23)	protein	128	4% helix, 50% strand	O34919
B, D, E	SPBC2 prophage-derived deoxyuridine 5'-triphosphate nucleo tidohydrolase yoss (EC 3.6.1.23)	protein	129	4% helix, 47% strand	O34919

Ligands and binding sites

UMP · 2'-deoxyuridine 5'-monophosphate · ligand · 6 copies · chains A, C, B, D, F, E
NA · Sodium ion · metal · 5 copies · chains A, B, F, C, D, E

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

Pockets

9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	662	0.72	0.79	55	UMP
2	717	0.70	0.77	65	UMP
3	246	0.55	0.77	30	UMP
4	231	0.54	0.77	31	UMP
5	153	0.48	0.77	30	UMP

Interfaces

8 interfaces between chains.

E–F · 1519 Å² buried · 21 hydrogen bonds · protein-protein
D–F · 1519 Å² buried · 22 hydrogen bonds · protein-protein
D–E · 1501 Å² buried · 20 hydrogen bonds · protein-protein
B–C · 1489 Å² buried · 20 hydrogen bonds · protein-protein
A–C · 1483 Å² buried · 20 hydrogen bonds · protein-protein

Compared structures

4AO5 · B. subtilis prophage dUTPase YosS in complex with dUMP · the same entry in another collection · chain F against F, TM-score 1.00
O34919 · AlphaFold monomer V2.0 prediction for spbeta prophage-derived deoxyuridine… · a predicted model of the same protein · chain B against A, TM-score 0.96

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 O34919
Elsewhere: RCSB PDB 4AO5 · PDBe 4AO5 · UniProt O34919

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