MolNFT v1 · #154326 · protein

Crystal structure of thymidylate synthase from shrimp

6K7R: “Crystal structure of thymidylate synthase from shrimp”. X-ray diffraction, 1 ligand (UMP), 8 pockets (best druggability 0.69). MolNFT v1 #154326 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6K7R
Type: protein
Length: 556 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Thymidylate synthase
EC: 2.1.1.45
UniProt: C6GJB8
Ligands: UMP
Pockets: 8 · best druggability 0.69

Structure

x-ray diffraction · 2 distinct chains · 34% helix, 24% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Thymidylate synthase (EC 2.1.1.45)	protein	275	35% helix, 24% strand	C6GJB8
B	Thymidylate synthase (EC 2.1.1.45)	protein	281	34% helix, 23% strand	C6GJB8

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

8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	555	0.69	0.78	50	UMP
2	293	0.60	0.78	40	UMP
3	107	0.40	0.76	18	empty
4	87	0.38	0.77	18	empty
5	57	0.31	0.76	20	empty

Interfaces

1 interface between chains.

A–B · 1964 Å² buried · 36 hydrogen bonds · protein-protein

Compared structures

6K7R · Crystal structure of thymidylate synthase from shrimp · 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 C6GJB8
Elsewhere: RCSB PDB 6K7R · PDBe 6K7R · UniProt C6GJB8

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