Research workbench

Crystal structure of MERS-cov S1 N-terminal domain

Analyse Crystal structure of MERS-cov S1 N-terminal domain in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5VYH
Type: protein
Length: 342 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: S protein
UniProt: T2B999
Ligands: FOL, NAG
Pockets: 3 · best druggability 0.70

Structure

x-ray diffraction · 1 distinct chain · 10% helix, 42% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	S protein	protein	342	10% helix, 42% strand	T2B999

Ligands and binding sites

FOL · Folic acid · ligand · chains A
NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains A
MPD · (4S)-2-methyl-2,4-pentanediol · additive · chains A
IMD · Imidazole · additive · chains A

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

Pockets

3 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	88	0.70	0.93	18	MPD
2	163	0.67	0.87	35	empty
3	51	0.25	0.73	18	empty

Modifications

Observed in the structure: 8 glycan, 4 disulfide (N-glycosylation, disulfide).

Compared structures

5VYH · Crystal Structure of MERS-CoV S1 N-terminal Domain · 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 T2B999
Elsewhere: RCSB PDB 5VYH · PDBe 5VYH · UniProt T2B999

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.