SMTL ID : 7pki.1

Crystal structure of human ACE2 bound to the spike receptor-binding domain from a cave bat sarbecovirus closely related to SARS-CoV-2.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.94 Å

Oligo State

hetero-1-1-mer

Ligands

1 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.1: 3 residues within 4Å: Chain A: K.8, N.72, T.74 No protein-ligand interaction detected (PLIP)

6 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.2: 5 residues within 4Å: Chain A: N.35, T.37, E.39, N.40, Q.322 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.35, A:T.37, A:E.39, A:N.40 NAG.3: 3 residues within 4Å: Chain A: F.267, N.414, W.576 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:F.267 NAG.4: 2 residues within 4Å: Chain A: S.402, N.528 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.528 NAG.5: 2 residues within 4Å: Chain A: K.291, N.304 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.291, A:N.304 NAG.13: 8 residues within 4Å: Chain B: F.7, G.8, N.12, V.36, L.37, Y.38, N.39 Ligands: NAG.14 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:V.36, B:L.37, B:N.39 NAG.14: 3 residues within 4Å: Chain B: N.39, T.41 Ligands: NAG.13 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.39

4 x SO4: SULFATE ION(Non-functional Binders)

SO4.6: 2 residues within 4Å: Chain A: T.37, E.38 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.38 SO4.7: 4 residues within 4Å: Chain A: F.256, D.349, T.353, E.388 No protein-ligand interaction detected (PLIP) SO4.8: 4 residues within 4Å: Chain A: A.330, H.360, D.364, H.383 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:A.330 Salt bridges: A:H.360, A:H.383 SO4.15: 2 residues within 4Å: Chain B: K.162, S.163 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.163 Salt bridges: B:K.162

1 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.9: 5 residues within 4Å: Chain A: A.278, G.404, L.405, L.406, S.407 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.282, A:L.406

5 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.10: 3 residues within 4Å: Chain A: H.177, Y.178, R.201 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.201, A:R.201 PEG.11: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) PEG.18: 8 residues within 4Å: Chain A: H.16, E.19, K.335 Chain B: R.72, Y.122, Y.164, G.165, Y.174 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:R.72, B:G.165, B:G.165, A:K.335 PEG.19: 3 residues within 4Å: Chain B: R.24, Y.65, F.133 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.24 PEG.20: 3 residues within 4Å: Chain B: Y.20, L.121, L.161 No protein-ligand interaction detected (PLIP)

1 x ZN: ZINC ION(Non-covalent)

ZN.12: 4 residues within 4Å: Chain A: R.255, H.327, H.487, Y.497 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:Y.497

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.16: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.17: 1 residues within 4Å: Chain B: K.47 Ligand excluded by PLIP

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.21: 2 residues within 4Å: Chain B: R.24, R.135 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.135, B:R.135

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Temmam, S. et al., Bat coronaviruses related to SARS-CoV-2 and infectious for human cells. Nature (2022)

Release Date

2022-01-19

Peptides

Processed angiotensin-converting enzyme 2: A
BANAL 236 coronavirus spike receptor-binding domain: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
E

Processed angiotensin-converting enzyme 2

BANAL 236 coronavirus spike receptor-binding domain

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