Research workbench

Human thymidylate synthase in complex with dump and methotrexate

Analyse Human thymidylate synthase in complex with dump and methotrexate in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5X66
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: UMP, MTX
Pockets: 20 · best druggability 0.82

Structure

x-ray diffraction · 2 distinct chains · 34% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, F	Thymidylate synthase (EC 2.1.1.45)	protein	288	34% helix, 23% strand	P04818
E	Thymidylate synthase (EC 2.1.1.45)	protein	287	34% helix, 23% strand	P04818

Ligands and binding sites

UMP · 2'-deoxyuridine 5'-monophosphate · ligand · 6 copies · chains A, D, B, E, C, F
MTX · Methotrexate · ligand · 6 copies · chains A, B, C, D, E, F

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

Pockets

20 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1053	0.82	0.83	91	UMP, MTX
2	910	0.81	0.83	79	UMP, MTX
3	544	0.78	0.85	49	UMP, MTX
4	550	0.78	0.85	50	UMP, MTX
5	591	0.77	0.83	55	UMP, MTX

Interfaces

7 interfaces between chains.

A–D · 2201 Å² buried · 33 hydrogen bonds · protein-protein
C–F · 2178 Å² buried · 30 hydrogen bonds · protein-protein
B–E · 2143 Å² buried · 32 hydrogen bonds · protein-protein
A–B · 321 Å² buried · 6 hydrogen bonds · protein-protein
A–C · 306 Å² buried · 5 hydrogen bonds · protein-protein

Compared structures

5X66 · Human thymidylate synthase in complex with dUMP and methotrexate · the same entry in another collection · chain B against B, TM-score 1.00
P04818 · AlphaFold monomer V2.0 prediction for thymidylate synthase (P04818) · a predicted model of the same protein · chain B 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 5X66 · PDBe 5X66 · UniProt P04818

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