MolNFT v1 · #175946 · protein

Crystal structure of tick-borne encephalitis virus methyltransferase

7D6M: “Crystal structure of tick-borne encephalitis virus methyltransferase”. X-ray diffraction, 1 ligand (SAM), 5 pockets (best druggability 0.67). MolNFT v1 #175946 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 7D6M
Type: protein
Length: 520 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Tick-borne encephalitis virus methyltransferase
Ligands: SAM
Pockets: 5 · best druggability 0.67

Structure

x-ray diffraction · 1 distinct chain · 37% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Tick-borne encephalitis virus methyltransferase	protein	260	37% helix, 18% strand	—

Ligands and binding sites

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

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

Pockets

5 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	518	0.67	0.78	47	SAM
2	545	0.66	0.77	52	SAM
3	181	0.53	0.78	34	empty
4	132	0.44	0.76	21	empty
5	70	0.30	0.74	20	empty

Interfaces

1 interface between chains.

A–B · 437 Å² buried · 5 hydrogen bonds · protein-protein

Compared structures

7D6M · Crystal structure of tick-borne encephalitis virus methyltransferase · the same entry in another collection · chain B against B, 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
Elsewhere: RCSB PDB 7D6M · PDBe 7D6M

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