7EKH: Angiotensin-converting enzyme 2

Structure of SARS-CoV-2 spike receptor-binding domain Y453F mutation complexed with human ACE2. Determined by X-ray diffraction at 2.4 Å resolution. Released 3 Nov 2021.

Method: X-ray diffraction
Resolution: 2.4 Å
Organisms: Homo sapiens, Severe acute respiratory syndrome coronavirus 2
Chains: 2
Atoms: 6,717
Mol. weight: 96.87 kDa
Ligands: ZN, NAG
Released: 3 Nov 2021

Explore 7EKH in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7EKH contains 51 α-helices and 29 β-strands across 2 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 38 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	21-52	32
α-helix	56-80	25
α-helix	85-87	3
α-helix	91-101	11
α-helix	104-107	4
α-helix	110-129	20
β-strand	131-133	3	1
β-strand	141-143	3	1
α-helix	144-148	5
α-helix	149-154	6
α-helix	158-168	11
α-helix	169-173	5
α-helix	174-193	20
α-helix	199-203	5
α-helix	204-207	4
β-strand	209	1	2
β-strand	217	1	2
α-helix	219-251	33
β-strand	260	1	3
α-helix	261	1
β-strand	262-263	2	4
α-helix	276-278	3
α-helix	279-282	4
α-helix	289-290	2
α-helix	294-299	6
α-helix	304-317	14
α-helix	320-324	5
α-helix	325-330	6
β-strand	332	1	5
β-strand	347-352	6	5
β-strand	355-359	5	5
α-helix	366-384	19
α-helix	390-392	3
α-helix	400-413	14
α-helix	415-420	6
α-helix	432-465	34
α-helix	470-472	3
α-helix	473-480	8
α-helix	481-485	5
β-strand	487-488	2	4
α-helix	499-502	4
α-helix	504-507	4
α-helix	514-532	19
α-helix	539-541	3
α-helix	548-558	11
α-helix	566-574	9
α-helix	582-598	17
α-helix	599-601	3
β-strand	607	1	3

Chain B: 13 helices, 18 β-strands

Element	Residues	Length	Sheet
α-helix	334	1
β-strand	335	1	6
α-helix	336	1
α-helix	339-342	4
α-helix	347-348	2
β-strand	349	1	7
α-helix	350-352	3
β-strand	354-358	5	7
β-strand	361	1	8
β-strand	362	1	6
α-helix	365-369	5
β-strand	376-380	5	7
β-strand	392	1	8
β-strand	394-403	10	7
α-helix	404-409	6
α-helix	417	1
α-helix	418-422	5
β-strand	431-437	7	7
α-helix	439-442	4
β-strand	448	1	9
β-strand	452-454	3	10
α-helix	460-462	3
α-helix	471-472	2
β-strand	473-474	2	11
β-strand	485	1	11
β-strand	488-489	2	11
β-strand	492-494	3	10
β-strand	497	1	9
α-helix	503-505	3
β-strand	507-516	10	7
β-strand	524	1	8

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Angiotensin-converting enzyme 2	A	protein	603	Homo sapiens	Q9BYF1 (AlphaFold model)
Spike protein S1	B	protein	229	Severe acute respiratory syndrome coronavirus 2	P0DTC2 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>7EKH_1 Angiotensin-converting enzyme 2 (chains A)
STIEEQAKTFLDKFNHEAEDLFYQSSLASWNYNTNITEENVQNMNNAGDKWSAFLKEQST
LAQMYPLQEIQNLTVKLQLQALQQNGSSVLSEDKSKRLNTILNTMSTIYSTGKVCNPDNP
QECLLLEPGLNEIMANSLDYNERLWAWESWRSEVGKQLRPLYEEYVVLKNEMARANHYED
YGDYWRGDYEVNGVDGYDYSRGQLIEDVEHTFEEIKPLYEHLHAYVRAKLMNAYPSYISP
IGCLPAHLLGDMWGRFWTNLYSLTVPFGQKPNIDVTDAMVDQAWDAQRIFKEAEKFFVSV
GLPNMTQGFWENSMLTDPGNVQKAVCHPTAWDLGKGDFRILMCTKVTMDDFLTAHHEMGH
IQYDMAYAAQPFLLRNGANEGFHEAVGEIMSLSAATPKHLKSIGLLSPDFQEDNETEINF
LLKQALTIVGTLPFTYMLEKWRWMVFKGEIPKDQWMKKWWEMKREIVGVVEPVPHDETYC
DPASLFHVSNDYSFIRYYTRTLYQFQFQEALCQAAKHEGPLHKCDISNSTEAGQKLFNML
RLGKSEPWTLALENVVGAKNMNVRPLLNYFEPLFTWLKDQNKNSFVGWSTDWSPYADHHH
HHH

Sequence of entity 2 (B), FASTA

>7EKH_2 Spike protein S1 (chains B)
RVQPTESIVRFPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFK
CYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNS
NNLDSKVGGNYNYLFRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQ
PTNGVGYQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNFHHHHHH

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	1
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	4

Primary citation

Molecular insights into receptor binding of recent emerging SARS-CoV-2 variants. Han, P., Su, C., Zhang, Y. et al. Nat Commun (2021) 12:6103-6103. DOI 10.1038/s41467-021-26401-w · PubMed

Other PDB entries of the same protein (UniProt Q9BYF1 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9SPA 1.79 Å, Apo ACE2 extracellular domain
28KD 2.02 Å, ACE2 extracellular domain in complex with the macrocyclic peptide GR3.1.2
8BYJ 2.07 Å, The structures of Ace2 in complex with bicyclic peptide inhibitor
8B9P 2.11 Å, ACE2 in complex with bicyclic peptide inhibitor
8XSF 2.16 Å, SARS-CoV-2 rbd + imcas-364 + hACE2
1R42 2.2 Å, Native Human Angiotensin Converting Enzyme-Related Carboxypeptidase (ACE2)
7JVO 2.2 Å, Importin alpha bound to the C-terminus of ACE2
8TOR 2.2 Å, ACE2-peptide 2 complex
9RVA 2.2 Å, Crystal structure of the extracellular part of human ACE2 in complex with the…
9UE7 2.27 Å, Cryo-EM structure of SARS-CoV-2 KP.2 spike in complex with ACE2
8TOQ 2.3 Å, ACE2-peptide 1 complex
8BFW 2.33 Å, The structures of Ace2 in complex with bicyclic peptide inhibitor

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