MolNFT v1 · #74865 · protein

Dengue 3 NS5 methyltransferase bound to the substrate S-adenosyl methionine

3P97 · Non-structural protein 5: “Dengue 3 NS5 methyltransferase bound to the substrate S-adenosyl methionine”. X-ray diffraction, 1 ligand (SAM), 5 pockets (best druggability 0.65). MolNFT v1 #74865 on GenesisL1: 3D structure, binding…

PDB: 3P97
Type: protein
Length: 512 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Non-structural protein 5
EC: 2.1.1.56, 2.1.1.57
UniProt: C1KBQ3
Ligands: SAM
Pockets: 5 · best druggability 0.65

Structure

x-ray diffraction · 1 distinct chain · 37% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	Non-structural protein 5 (EC 2.1.1.56, 2.1.1.57)	protein	256	37% helix, 16% strand	C1KBQ3

Ligands and binding sites

SAM · S-adenosylmethionine · ligand · 2 copies · chains A, C

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

Pockets

5 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	532	0.65	0.77	50	SAM
2	504	0.65	0.77	47	SAM
3	59	0.41	0.82	18	empty
4	118	0.36	0.73	22	empty
5	54	0.24	0.72	14	empty

Interfaces

1 interface between chains.

A–C · 532 Å² buried · 5 hydrogen bonds · protein-protein

Compared structures

3P97 · Dengue 3 NS5 Methyltransferase bound to the substrate S-Adenosyl methionine · 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 C1KBQ3
Elsewhere: RCSB PDB 3P97 · PDBe 3P97 · UniProt C1KBQ3

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