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Thymidylate synthase from staphylococcus aureus.

Analyse Thymidylate synthase from staphylococcus aureus. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4DQ1
Type: protein
Length: 612 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Thymidylate synthase
EC: 2.1.1.45
UniProt: P67046
Ligands: UMP
Pockets: 9 · best druggability 0.68

Structure

x-ray diffraction · 2 distinct chains · 40% helix, 22% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Thymidylate synthase (EC 2.1.1.45)	protein	312	41% helix, 22% strand	P67046
B	Thymidylate synthase (EC 2.1.1.45)	protein	300	39% helix, 23% strand	P67046

Ligands and binding sites

UMP · 2'-deoxyuridine 5'-monophosphate · ligand · 2 copies · chains A, B

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

Pockets

9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	405	0.68	0.80	39	UMP
2	542	0.68	0.78	50	UMP
3	50	0.51	0.88	20	empty
4	84	0.47	0.82	13	empty
5	96	0.45	0.79	16	empty

Interfaces

1 interface between chains.

A–B · 2478 Å² buried · 45 hydrogen bonds · protein-protein

Compared structures

4DQ1 · Thymidylate synthase from Staphylococcus aureus. · the same entry in another collection · chain A against A, TM-score 1.00
P67046 · AlphaFold monomer V2.0 prediction for thymidylate synthase (P67046) · a predicted model of the same protein · chain B 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 P67046
Elsewhere: RCSB PDB 4DQ1 · PDBe 4DQ1 · UniProt P67046

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