MolNFT v1 · #139095 · protein

Structure of the N-terminal domain (ntd) of MERS-cov spike protein

5X4R · S protein: “Structure of the N-terminal domain (ntd) of MERS-cov spike protein”. X-ray diffraction, 1 ligand (NAG), 4 pockets (best druggability 0.75). MolNFT v1 #139095 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5X4R
Type: protein
Length: 333 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: S protein
UniProt: W6A028
Ligands: NAG
Pockets: 4 · best druggability 0.75

Structure

x-ray diffraction · 1 distinct chain · 11% helix, 41% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	S protein	protein	333	11% helix, 41% strand	W6A028

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A

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

Pockets

4 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	71	0.75	0.98	18	empty
2	124	0.70	0.91	29	empty
3	62	0.32	0.75	12	empty
4	52	0.27	0.74	18	empty

Modifications

Observed in the structure: 4 disulfide, 2 glycan (disulfide, N-glycosylation).

Compared structures

5X4R · Structure of the N-terminal domain (NTD) of MERS-CoV spike protein · 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 W6A028
Elsewhere: RCSB PDB 5X4R · PDBe 5X4R · UniProt W6A028

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