MolNFT v1 · #120532 · protein

Structural analysis of kshv thymidylate synthase

5H39 · ORF70: “Structural analysis of kshv thymidylate synthase”. X-ray diffraction, 1 ligand (UMP), 4 pockets (best druggability 0.70). MolNFT v1 #120532 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5H39
Type: protein
Length: 568 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: ORF70
UniProt: F5HBQ9
Ligands: UMP
Pockets: 4 · best druggability 0.70

Structure

x-ray diffraction · 2 distinct chains · 35% helix, 24% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	ORF70	protein	285	35% helix, 23% strand	F5HBQ9
B	ORF70	protein	283	35% helix, 24% strand	F5HBQ9

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

4 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	507	0.70	0.80	38	UMP
2	487	0.67	0.78	49	UMP
3	255	0.53	0.76	48	empty
4	56	0.28	0.74	15	empty

Interfaces

1 interface between chains.

A–B · 2159 Å² buried · 32 hydrogen bonds · protein-protein

Compared structures

5H39 · Structural analysis of KSHV thymidylate synthase · 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 F5HBQ9
Elsewhere: RCSB PDB 5H39 · PDBe 5H39 · UniProt F5HBQ9

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