Research workbench

E. COLI thymidylate synthase complexed with 5-nitro-2'-deoxy uridine

Analyse E. COLI thymidylate synthase complexed with 5-nitro-2'-deoxy uridine in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3B9H
Type: protein
Length: 264 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Thymidylate synthase
EC: 2.1.1.45
UniProt: P0A884
Ligands: NDU, PO4
Pockets: 1 · best druggability 0.74

Structure

x-ray diffraction · 1 distinct chain · 36% helix, 26% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Thymidylate synthase (EC 2.1.1.45)	protein	264	36% helix, 26% strand	P0A884

Ligands and binding sites

NDU · 2'-deoxy-5-nitrouridine 5'-monophosphate · ligand · chains A
PO4 · Phosphate ion · ion · 2 copies · chains A

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

Pockets

1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	453	0.74	0.83	45	NDU

Modifications

Observed in the structure: 1 covalent, 1 modified (covalent ligand, carboxylation).

Compared structures

3B9H · E. coli thymidylate synthase complexed with 5-NITRO-2'-DEOXY URIDINE · 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 P0A884
Elsewhere: RCSB PDB 3B9H · PDBe 3B9H · UniProt P0A884

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