SMTL ID : 6m17.1

The 2019-nCoV RBD/ACE2-B0AT1 complex

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-2-2-mer

Ligands

14 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: N.278, T.280, E.281 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 3 residues within 4Å: Chain B: N.62, N.67, Q.349 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 2 residues within 4Å: Chain B: K.35, N.99 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 3 residues within 4Å: Chain B: Q.110, Q.111, N.112 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 3 residues within 4Å: Chain B: F.294, N.441, W.603 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 2 residues within 4Å: Chain B: K.322, N.555 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 5 residues within 4Å: Chain B: D.145, N.168, N.699, S.701, D.702 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 3 residues within 4Å: Chain D: N.278, T.280, E.281 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 3 residues within 4Å: Chain E: N.62, N.67, Q.349 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 2 residues within 4Å: Chain E: K.35, N.99 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 3 residues within 4Å: Chain E: Q.110, Q.111, N.112 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 3 residues within 4Å: Chain E: F.294, N.441, W.603 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 2 residues within 4Å: Chain E: K.322, N.555 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 5 residues within 4Å: Chain E: D.145, N.168, N.699, S.701, D.702 No protein-ligand interaction detected (PLIP)

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

NAG-NAG-NAG.8: 1 residues within 4Å: Chain C: N.25 No protein-ligand interaction detected (PLIP) NAG-NAG-NAG.16: 1 residues within 4Å: Chain F: N.25 No protein-ligand interaction detected (PLIP)

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

NAG.17: 1 residues within 4Å: Chain A: N.178 No protein-ligand interaction detected (PLIP) NAG.18: 3 residues within 4Å: Chain A: R.198, N.202, N.496 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.198, A:N.496 NAG.19: 2 residues within 4Å: Chain A: G.373, N.374 No protein-ligand interaction detected (PLIP) NAG.20: 1 residues within 4Å: Chain A: N.388 No protein-ligand interaction detected (PLIP) NAG.22: 2 residues within 4Å: Chain B: K.318, N.331 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.318 NAG.24: 1 residues within 4Å: Chain D: N.178 No protein-ligand interaction detected (PLIP) NAG.25: 3 residues within 4Å: Chain D: R.198, N.202, N.496 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:R.198, D:N.496 NAG.26: 2 residues within 4Å: Chain D: G.373, N.374 No protein-ligand interaction detected (PLIP) NAG.27: 1 residues within 4Å: Chain D: N.388 No protein-ligand interaction detected (PLIP) NAG.29: 2 residues within 4Å: Chain E: K.318, N.331 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:K.318

2 x LEU: LEUCINE(Non-covalent)

LEU.21: 12 residues within 4Å: Chain A: F.68, C.69, V.70, G.71, L.72, Y.149, F.297, S.298, S.300, F.303, S.451, N.455 5 PLIP interactions: 5 interactions with chain A, Hydrophobic interactions: A:F.68, A:Y.149, A:F.303 Hydrogen bonds: A:L.72, A:F.297 LEU.28: 12 residues within 4Å: Chain D: F.68, C.69, V.70, G.71, L.72, Y.149, F.297, S.298, S.300, F.303, S.451, N.455 5 PLIP interactions: 5 interactions with chain D, Hydrophobic interactions: D:F.68, D:Y.149, D:F.303 Hydrogen bonds: D:L.72, D:F.297

2 x ZN: ZINC ION(Non-covalent)

ZN.23: 4 residues within 4Å: Chain B: H.383, E.384, H.387, E.411 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:H.383, B:E.411 ZN.30: 4 residues within 4Å: Chain E: H.383, E.384, H.387, E.411 2 PLIP interactions: 2 interactions with chain E Metal complexes: E:H.383, E:E.411

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yan, R. et al., Structural basis for the recognition of SARS-CoV-2 by full-length human ACE2. Science (2020)

Release Date

2020-03-11

Peptides

Sodium-dependent neutral amino acid transporter B(0)AT1: AD
Angiotensin-converting enzyme 2: BE
Spike protein S1: CF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

D
C

B
B

E
D

C
E

F
F

Membrane

We predict this structure to be a membrane protein.
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Sodium-dependent neutral amino acid transporter B(0)AT1

Angiotensin-converting enzyme 2

Spike protein S1

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