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Structure determination of the rbd-NB1A7

Analyse Structure determination of the rbd-NB1A7 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7FAT
Type: protein
Length: 316 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Spike protein S1; NB_1A7
UniProt: P0DTC2
Ligands: NAG
Pockets: 2 · best druggability 0.32

Structure

x-ray diffraction · 2 distinct chains · 16% helix, 40% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Spike protein S1	protein	184	18% helix, 33% strand	P0DTC2
B	NB_1A7	protein	132	12% helix, 49% strand	—

Ligands and binding sites

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

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

Pockets

2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	71	0.32	0.75	22	empty
2	53	0.31	0.77	12	empty

Interfaces

1 interface between chains.

A–B · 797 Å² buried · 21 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 5 disulfide, 1 glycan (disulfide, N-glycosylation).

Compared structures

7FAT · Structure Determination of the RBD-NB1A7 · 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 P0DTC2
Elsewhere: RCSB PDB 7FAT · PDBe 7FAT · UniProt P0DTC2

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