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Trapping of an oxocarbenium ion intermediate in up crystals

Analyse Trapping of an oxocarbenium ion intermediate in up crystals in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3KVV
Type: protein
Length: 1,452 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Uridine phosphorylase
EC: 2.4.2.3
UniProt: P12758
Ligands: URF, R2B, SO4
Pockets: 15 · best druggability 0.80

Structure

x-ray diffraction · 6 distinct chains · 33% helix, 30% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Uridine phosphorylase (EC 2.4.2.3)	protein	243	33% helix, 30% strand	P12758
B	Uridine phosphorylase (EC 2.4.2.3)	protein	243	34% helix, 30% strand	P12758
C	Uridine phosphorylase (EC 2.4.2.3)	protein	241	33% helix, 30% strand	P12758
D	Uridine phosphorylase (EC 2.4.2.3)	protein	240	33% helix, 30% strand	P12758
E	Uridine phosphorylase (EC 2.4.2.3)	protein	247	34% helix, 30% strand	P12758
F	Uridine phosphorylase (EC 2.4.2.3)	protein	238	33% helix, 31% strand	P12758

Ligands and binding sites

URF · 5-fluorouracil · ligand · 6 copies · chains A, B, C, D, E, F
R2B · 1,4-anhydro-D-erythro-pent-1-enitol · ligand · 6 copies · chains A, B, C, D, E, F
SO4 · Sulfate ion · ion · 6 copies · chains A, B, C, D, E, F

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

Pockets

15 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	962	0.80	0.82	111	empty
2	255	0.65	0.82	30	URF, SO4, R2B
3	245	0.64	0.82	36	URF, SO4, R2B
4	186	0.63	0.84	28	URF, SO4, R2B
5	173	0.62	0.84	32	URF, SO4, R2B

Interfaces

12 interfaces between chains.

A–B · 2025 Å² buried · 19 hydrogen bonds · protein-protein
E–F · 1998 Å² buried · 18 hydrogen bonds · protein-protein
C–D · 1990 Å² buried · 20 hydrogen bonds · protein-protein
A–C · 1045 Å² buried · 4 hydrogen bonds · protein-protein
D–E · 1039 Å² buried · 4 hydrogen bonds · protein-protein

Compared structures

3KVV · Trapping of an oxocarbenium ion intermediate in UP crystals · the same entry in another collection · chain F against F, TM-score 1.00
P12758 · AlphaFold monomer V2.0 prediction for uridine phosphorylase (P12758) · a predicted model of the same protein · 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 P12758
Elsewhere: RCSB PDB 3KVV · PDBe 3KVV · UniProt P12758

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