MolNFT v1 · #172281 · protein

Crystal structure of his-tagged human thymidylate synthase (ht-hts) in complex with fdump and raltitrexed (tomudex)

6ZXO: “Crystal structure of his-tagged human thymidylate synthase (ht-hts) in complex with fdump and raltitrexed…”. X-ray diffraction, 2 ligands (D16, UFP), 20 pockets (best druggability 0.84). MolNFT v1 #172281 on GenesisL1: 3D structure…

PDB: 6ZXO
Type: protein
Length: 1,727 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Thymidylate synthase
EC: 2.1.1.45
UniProt: P04818
Ligands: D16, UFP
Pockets: 20 · best druggability 0.84

Structure

x-ray diffraction · 2 distinct chains · 33% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E	Thymidylate synthase (EC 2.1.1.45)	protein	288	33% helix, 23% strand	P04818
F	Thymidylate synthase (EC 2.1.1.45)	protein	287	32% helix, 23% strand	P04818

Ligands and binding sites

D16 · Tomudex · ligand · 6 copies · chains A, B, C, D, E, F
UFP · 5-fluoro-2'-deoxyuridine-5'-monophosphate · ligand · 6 copies · chains A, B, C, D, E, F
EDO · 1,2-ethanediol · additive · 3 copies · chains A, B, C

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

Pockets

20 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1085	0.84	0.85	103	D16, UFP
2	343	0.79	0.89	42	D16, UFP
3	632	0.78	0.83	60	D16, UFP
4	332	0.78	0.89	37	D16, UFP
5	463	0.76	0.84	44	D16, UFP

Interfaces

7 interfaces between chains.

C–D · 2168 Å² buried · 36 hydrogen bonds · protein-protein
A–B · 2150 Å² buried · 32 hydrogen bonds · protein-protein
E–F · 2122 Å² buried · 33 hydrogen bonds · protein-protein
D–E · 281 Å² buried · 2 hydrogen bonds · protein-protein
A–C · 228 Å² buried · 1 hydrogen bond · protein-protein

Modifications

Observed in the structure: 1 modified (artifact).

Compared structures

6ZXO · Crystal structure of His-tagged human thymidylate synthase (HT-hTS) in complex with FdUMP… · the same entry in another collection · chain F against F, TM-score 1.00
P04818 · AlphaFold monomer V2.0 prediction for thymidylate synthase (P04818) · a predicted model of the same protein · chain C against A, TM-score 0.99

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 6ZXO · PDBe 6ZXO · UniProt P04818

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