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Wild-type human thymidylate synthase with bound purpurogallin

Analyse Wild-type human thymidylate synthase with bound purpurogallin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4GD7
Type: protein
Length: 273 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Thymidylate synthase
EC: 2.1.1.45
UniProt: P04818
Ligands: TIY, SO4
Pockets: 4 · best druggability 0.59

Structure

x-ray diffraction · 1 distinct chain · 33% helix, 25% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Thymidylate synthase (EC 2.1.1.45)	protein	273	33% helix, 25% strand	P04818

Ligands and binding sites

TIY · 2,3,4,6-tetrahydroxy-5H-benzo[7]annulen-5-one · ligand · chains A
SO4 · Sulfate ion · ion · 3 copies · chains A
EDO · 1,2-ethanediol · additive · chains A

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	311	0.59	0.77	28	empty
2	59	0.34	0.77	12	empty
3	73	0.32	0.74	18	empty
4	64	0.29	0.74	14	empty

Modifications

Observed in the structure: 3 modified (artifact, oxidation).

Compared structures

4GD7 · Wild-Type Human Thymidylate Synthase with bound Purpurogallin · 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 P04818
Elsewhere: RCSB PDB 4GD7 · PDBe 4GD7 · UniProt P04818

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