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Crystal structure of uridine bound to geobacillus thermoglucosidasius pyrimidine nucleoside phosphorylase pynp

Analyse Crystal structure of uridine bound to geobacillus thermoglucosidasius… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7M7K
Type: protein
Length: 432 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Pyrimidine-nucleoside phosphorylase
EC: 2.4.2.2
UniProt: A0A369WPE5
Ligands: URI, SO4
Pockets: 5 · best druggability 0.76

Structure

x-ray diffraction · 1 distinct chain · 46% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
B	Pyrimidine-nucleoside phosphorylase (EC 2.4.2.2)	protein	432	46% helix, 16% strand	A0A369WPE5

Ligands and binding sites

URI · Uridine · ligand · chains B
SO4 · Sulfate ion · ion · 3 copies · chains B

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

Pockets

5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	97	0.76	0.97	27	empty
2	784	0.71	0.77	58	SO4, URI
3	113	0.51	0.81	17	empty
4	94	0.42	0.78	20	empty
5	54	0.27	0.74	18	empty

Compared structures

7M7K · Crystal structure of uridine bound to Geobacillus thermoglucosidasius pyrimidine… · the same entry in another collection · chain B against B, 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 A0A369WPE5
Elsewhere: RCSB PDB 7M7K · PDBe 7M7K · UniProt A0A369WPE5

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