MolNFT v1 · #167810 · protein

Structure of SARS-cov-2 chimeric receptor-binding domain complexed with its receptor human ACE2

6VW1 · Angiotensin-converting enzyme 2: “Structure of SARS-cov-2 chimeric receptor-binding domain complexed with its receptor human ACE2”. X-ray diffraction, 4 ligands (NAG, BMA, ZN), 12 pockets (best druggability 0.77). MolNFT v1 #167810…

PDB: 6VW1
Type: protein
Length: 1,579 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Angiotensin-converting enzyme 2; SARS-cov-2 chimeric rbd
EC: 3.4.17.23, 3.4.17.-
UniProt: Q9BYF1, P59594, P0DTC2
Ligands: NAG, BMA, ZN, CL
Pockets: 12 · best druggability 0.77

Structure

x-ray diffraction · 3 distinct chains · 44% helix, 13% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Angiotensin-converting enzyme 2 (EC 3.4.17.23, 3.4.17.-)	protein	596	63% helix, 4% strand	Q9BYF1
E	SARS-cov-2 chimeric rbd	protein	193	15% helix, 27% strand	P59594, P0DTC2
F	SARS-cov-2 chimeric rbd	protein	194	17% helix, 27% strand	P59594, P0DTC2

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 22 copies · chains A, B, E, F
BMA · beta-D-mannopyranose · sugar · 4 copies · chains E
ZN · Zinc ion · metal · 2 copies · chains A, B
CL · Chloride ion · ion · 2 copies · chains A, B
EDO · 1,2-ethanediol · additive · 4 copies · chains A, B

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

Pockets

12 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	562	0.77	0.84	51	ZN
2	616	0.74	0.81	86	ZN
3	415	0.63	0.77	62	empty
4	210	0.63	0.82	26	empty
5	315	0.60	0.78	41	empty

Interfaces

3 interfaces between chains.

B–F · 995 Å² buried · 17 hydrogen bonds · protein-protein
A–E · 947 Å² buried · 15 hydrogen bonds · protein-protein
A–B · 196 Å² buried · 4 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 13 disulfide, 12 glycan (disulfide, N-glycosylation).

Compared structures

6VW1 · Structure of SARS-CoV-2 chimeric receptor-binding domain complexed with its receptor… · the same entry in another collection · chain B against B, TM-score 1.00
Q9BYF1 · AlphaFold monomer V2.0 prediction for angiotensin-converting enzyme 2 (Q9BYF1) · a predicted model of the same protein · chain A against A, TM-score 0.99
3SCI · Crystal structure of spike protein receptor-binding domain from a predicted SARS… · a predicted model of the same protein · chain A against A, TM-score 0.98
3SCI · Crystal structure of spike protein receptor-binding domain from a predicted SARS… · a predicted model of the same protein · chain A against A, TM-score 0.98
3SCJ · Crystal structure of spike protein receptor-binding domain from a predicted SARS… · a predicted model of the same protein · chain A against A, TM-score 0.97
3SCJ · Crystal structure of spike protein receptor-binding domain from a predicted SARS… · a predicted model of the same protein · chain A against A, TM-score 0.97
3SCK · Crystal structure of spike protein receptor-binding domain from a predicted SARS… · a predicted model of the same protein · chain A against A, TM-score 0.97
3SCK · Crystal structure of spike protein receptor-binding domain from a predicted SARS… · a predicted model of the same protein · chain A against A, TM-score 0.97

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 Q9BYF1
Every structure of UniProt P59594
Every structure of UniProt P0DTC2
Elsewhere: RCSB PDB 6VW1 · PDBe 6VW1 · UniProt Q9BYF1 · UniProt P59594 · UniProt P0DTC2

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