MolNFT v1 · #37650 · protein

Lactobacillus casei Y261M in complex with substrate, dump

2G8A · Thymidylate synthase: “Lactobacillus casei Y261M in complex with substrate, dump”. X-ray diffraction, 1 ligand (UMP), 2 pockets (best druggability 0.71). MolNFT v1 #37650 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 2G8A
Type: protein
Length: 316 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Thymidylate synthase
EC: 2.1.1.45
UniProt: P00469
Ligands: UMP
Pockets: 2 · best druggability 0.71

Structure

x-ray diffraction · 1 distinct chain · 39% helix, 22% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Thymidylate synthase (EC 2.1.1.45)	protein	316	39% helix, 22% strand	P00469

Ligands and binding sites

UMP · 2'-deoxyuridine 5'-monophosphate · ligand · chains A

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

Pockets

2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	745	0.71	0.77	50	UMP
2	117	0.56	0.83	18	empty

Compared structures

2G8A · Lactobacillus casei Y261M in complex with substrate, dUMP · the same entry in another collection · chain A against A, TM-score 1.00
P00469 · AlphaFold monomer V2.0 prediction for thymidylate synthase (P00469) · a predicted model of the same protein · chain A 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 P00469
Elsewhere: RCSB PDB 2G8A · PDBe 2G8A · UniProt P00469

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