MolNFT v1 · #30795 · protein

E. COLI ts complexed with dump and inhibitor GA9

2A9W · Thymidylate synthase: “E. COLI ts complexed with dump and inhibitor GA9”. X-ray diffraction, 4 ligands (UMP, GA9, 2BR), 16 pockets (best druggability 0.73). MolNFT v1 #30795 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 2A9W
Type: protein
Length: 1,056 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Thymidylate synthase
EC: 2.1.1.45
UniProt: P0A884
Ligands: UMP, GA9, 2BR, PO4
Pockets: 16 · best druggability 0.73

Structure

x-ray diffraction · 1 distinct chain · 34% helix, 26% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Thymidylate synthase (EC 2.1.1.45)	protein	264	34% helix, 26% strand	P0A884

Ligands and binding sites

UMP · 2'-deoxyuridine 5'-monophosphate · ligand · 4 copies · chains A, B, C, D
GA9 · 3,3-bis(3-bromo-4-hydroxyphenyl)-7-chloro-1H,3H-benzo[de]isochromen-1-one · ligand · 4 copies · chains A, B, C, D
2BR · 2-bromophenol · ligand · chains B
PO4 · Phosphate ion · ion · 12 copies · chains A, B, C, D
GOL · Glycerol · additive · 10 copies · chains A, B, C, D
BME · Beta-mercaptoethanol · additive · 4 copies · chains A, C, D

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	629	0.73	0.80	49	PO4, UMP, GA9, GOL
2	658	0.72	0.79	57	PO4, UMP, GA9, GOL, BME
3	685	0.71	0.78	56	PO4, UMP, GA9, GOL, BME
4	698	0.70	0.77	51	PO4, UMP, GA9, GOL, BME
5	465	0.65	0.77	50	2BR, GOL

Interfaces

3 interfaces between chains.

C–D · 2414 Å² buried · 39 hydrogen bonds · protein-protein
A–B · 2283 Å² buried · 29 hydrogen bonds · protein-protein
B–D · 288 Å² buried · 4 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 5 covalent, 4 modified (additive adduct, carboxylation).

Compared structures

2A9W · E. coli TS complexed with dUMP and inhibitor GA9 · the same entry in another collection · chain A against A, TM-score 1.00
P0A884 · AlphaFold monomer V2.0 prediction for thymidylate synthase (P0A884) · 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 P0A884
Elsewhere: RCSB PDB 2A9W · PDBe 2A9W · UniProt P0A884

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