MolNFT v1 · #174194 · protein

Crystal structure of the SARS-cov-2 receptor binding domain in complex with antibody ion-300

7BNV · Surface glycoprotein: “Crystal structure of the SARS-cov-2 receptor binding domain in complex with antibody ion-300”. X-ray diffraction, 1 ligand (NAG), 6 pockets (best druggability 0.61). MolNFT v1 #174194 on GenesisL1: 3D…

PDB: 7BNV
Type: protein
Length: 633 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Surface glycoprotein; Heavy chain; Light chain
UniProt: A0A6M5UN06
Ligands: NAG
Pockets: 6 · best druggability 0.61

Structure

x-ray diffraction · 3 distinct chains · 8% helix, 43% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Surface glycoprotein	protein	194	13% helix, 30% strand	A0A6M5UN06
H	Heavy chain	protein	223	7% helix, 49% strand	—
L	Light chain	protein	216	6% helix, 49% strand	—

Ligands and binding sites

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

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

Pockets

6 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	352	0.61	0.78	52	empty
2	214	0.58	0.80	27	empty
3	329	0.53	0.74	46	empty
4	121	0.40	0.75	28	empty
5	65	0.32	0.75	16	empty

Interfaces

3 interfaces between chains.

H–L · 1819 Å² buried · 11 hydrogen bonds · protein-protein
A–H · 710 Å² buried · 8 hydrogen bonds · protein-protein
A–L · 57 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 disulfide, 1 glycan (disulfide, N-glycosylation).

Compared structures

7BNV · Crystal Structure of the SARS-CoV-2 Receptor Binding Domain in Complex with Antibody… · 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 A0A6M5UN06
Elsewhere: RCSB PDB 7BNV · PDBe 7BNV · UniProt A0A6M5UN06

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