MolNFT v1 · #91831 · protein

Crystal structure of mtb thya in complex with dump and raltitrexed

4FOX · Thymidylate synthase: “Crystal structure of mtb thya in complex with dump and raltitrexed”. X-ray diffraction, 2 ligands (D16, UMP), 20 pockets (best druggability 0.77). MolNFT v1 #91831 on GenesisL1: 3D structure, binding sites and…

PDB: 4FOX
Type: protein
Length: 2,086 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Thymidylate synthase
EC: 2.1.1.45
UniProt: P67044
Ligands: D16, UMP
Pockets: 20 · best druggability 0.77

Structure

x-ray diffraction · 4 distinct chains · 36% helix, 26% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, F	Thymidylate synthase (EC 2.1.1.45)	protein	261	35% helix, 26% strand	P67044
D	Thymidylate synthase (EC 2.1.1.45)	protein	263	36% helix, 26% strand	P67044
E, G	Thymidylate synthase (EC 2.1.1.45)	protein	260	37% helix, 26% strand	P67044
H	Thymidylate synthase (EC 2.1.1.45)	protein	259	35% helix, 25% strand	P67044

Ligands and binding sites

D16 · Tomudex · ligand · 8 copies · chains A, B, C, D, E, F, G, H
UMP · 2'-deoxyuridine 5'-monophosphate · ligand · 8 copies · chains A, B, C, D, E, F, G, H

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	423	0.77	0.86	45	D16, UMP
2	136	0.73	0.93	35	empty
3	413	0.72	0.82	44	UMP, D16
4	490	0.71	0.81	49	D16, UMP
5	474	0.71	0.81	46	D16, UMP

Interfaces

9 interfaces between chains.

A–B · 2193 Å² buried · 33 hydrogen bonds · protein-protein
C–D · 2175 Å² buried · 30 hydrogen bonds · protein-protein
E–F · 2172 Å² buried · 30 hydrogen bonds · protein-protein
G–H · 2098 Å² buried · 33 hydrogen bonds · protein-protein
A–D · 820 Å² buried · 14 hydrogen bonds · protein-protein

Compared structures

4FOX · Crystal Structure of Mtb ThyA in complex with dUMP and Raltitrexed · the same entry in another collection · chain G against G, 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 P67044
Elsewhere: RCSB PDB 4FOX · PDBe 4FOX · UniProt P67044

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