SMTL ID : 7dwx.1

Conformation 1 of S-ACE2-B0AT1 ternary complex

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-2-6-mer

Ligands

58 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.65, N.70, Q.352 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 2 residues within 4Å: Chain B: K.38, N.102 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 3 residues within 4Å: Chain B: Q.113, Q.114, N.115 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 3 residues within 4Å: Chain B: F.297, N.444, W.606 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 2 residues within 4Å: Chain B: K.325, N.558 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 5 residues within 4Å: Chain B: D.148, N.171, N.702, S.704, D.705 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 3 residues within 4Å: Chain C: N.278, T.280, E.281 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 3 residues within 4Å: Chain D: N.65, N.70, Q.352 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 2 residues within 4Å: Chain D: K.38, N.102 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 3 residues within 4Å: Chain D: Q.113, Q.114, N.115 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 3 residues within 4Å: Chain D: F.297, N.444, W.606 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 2 residues within 4Å: Chain D: K.325, N.558 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 5 residues within 4Å: Chain D: D.148, N.171, N.702, S.704, D.705 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 2 residues within 4Å: Chain E: N.331, Q.580 No protein-ligand interaction detected (PLIP) NAG-NAG.16: 1 residues within 4Å: Chain E: N.343 No protein-ligand interaction detected (PLIP) NAG-NAG.17: 4 residues within 4Å: Chain E: N.717, L.922, Q.926, Q.1071 1 PLIP interactions: 1 interactions with chain E Hydrophobic interactions: E:L.922 NAG-NAG.18: 3 residues within 4Å: Chain E: N.801, S.803, Q.804 No protein-ligand interaction detected (PLIP) NAG-NAG.19: 3 residues within 4Å: Chain E: A.706, E.1072, N.1074 No protein-ligand interaction detected (PLIP) NAG-NAG.20: 3 residues within 4Å: Chain E: N.1098, T.1100, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG.21: 1 residues within 4Å: Chain E: N.1134 No protein-ligand interaction detected (PLIP) NAG-NAG.22: 3 residues within 4Å: Chain F: N.331, P.579, Q.580 No protein-ligand interaction detected (PLIP) NAG-NAG.23: 2 residues within 4Å: Chain F: F.342, N.343 No protein-ligand interaction detected (PLIP) NAG-NAG.24: 3 residues within 4Å: Chain F: N.709, G.1131 Chain G: D.796 No protein-ligand interaction detected (PLIP) NAG-NAG.25: 3 residues within 4Å: Chain F: N.717, L.922, Q.926 1 PLIP interactions: 1 interactions with chain F Hydrophobic interactions: F:L.922 NAG-NAG.26: 3 residues within 4Å: Chain F: N.801, S.803, Q.804 No protein-ligand interaction detected (PLIP) NAG-NAG.27: 4 residues within 4Å: Chain F: N.1098, T.1100, H.1101, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG.28: 1 residues within 4Å: Chain F: N.1134 No protein-ligand interaction detected (PLIP) NAG-NAG.29: 2 residues within 4Å: Chain G: N.331, Q.580 No protein-ligand interaction detected (PLIP) NAG-NAG.30: 2 residues within 4Å: Chain G: F.342, N.343 No protein-ligand interaction detected (PLIP) NAG-NAG.31: 2 residues within 4Å: Chain E: D.796 Chain G: N.709 No protein-ligand interaction detected (PLIP) NAG-NAG.32: 5 residues within 4Å: Chain G: N.717, L.922, N.925, Q.926, Q.1071 2 PLIP interactions: 2 interactions with chain G Hydrophobic interactions: G:L.922, G:N.925 NAG-NAG.33: 2 residues within 4Å: Chain G: N.801, S.803 No protein-ligand interaction detected (PLIP) NAG-NAG.34: 3 residues within 4Å: Chain G: A.706, E.1072, N.1074 No protein-ligand interaction detected (PLIP) NAG-NAG.35: 4 residues within 4Å: Chain G: N.1098, T.1100, H.1101, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG.36: 1 residues within 4Å: Chain G: N.1134 No protein-ligand interaction detected (PLIP) NAG-NAG.37: 2 residues within 4Å: Chain H: N.331, Q.580 No protein-ligand interaction detected (PLIP) NAG-NAG.38: 1 residues within 4Å: Chain H: N.343 No protein-ligand interaction detected (PLIP) NAG-NAG.39: 4 residues within 4Å: Chain H: N.717, L.922, Q.926, Q.1071 1 PLIP interactions: 1 interactions with chain H Hydrophobic interactions: H:L.922 NAG-NAG.40: 3 residues within 4Å: Chain H: N.801, S.803, Q.804 No protein-ligand interaction detected (PLIP) NAG-NAG.41: 3 residues within 4Å: Chain H: A.706, E.1072, N.1074 No protein-ligand interaction detected (PLIP) NAG-NAG.42: 3 residues within 4Å: Chain H: N.1098, T.1100, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG.43: 1 residues within 4Å: Chain H: N.1134 No protein-ligand interaction detected (PLIP) NAG-NAG.44: 3 residues within 4Å: Chain I: N.331, P.579, Q.580 No protein-ligand interaction detected (PLIP) NAG-NAG.45: 2 residues within 4Å: Chain I: F.342, N.343 No protein-ligand interaction detected (PLIP) NAG-NAG.46: 3 residues within 4Å: Chain I: N.709, G.1131 Chain J: D.796 No protein-ligand interaction detected (PLIP) NAG-NAG.47: 3 residues within 4Å: Chain I: N.717, L.922, Q.926 1 PLIP interactions: 1 interactions with chain I Hydrophobic interactions: I:L.922 NAG-NAG.48: 3 residues within 4Å: Chain I: N.801, S.803, Q.804 No protein-ligand interaction detected (PLIP) NAG-NAG.49: 4 residues within 4Å: Chain I: N.1098, T.1100, H.1101, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG.50: 1 residues within 4Å: Chain I: N.1134 No protein-ligand interaction detected (PLIP) NAG-NAG.51: 2 residues within 4Å: Chain J: N.331, Q.580 No protein-ligand interaction detected (PLIP) NAG-NAG.52: 2 residues within 4Å: Chain J: F.342, N.343 No protein-ligand interaction detected (PLIP) NAG-NAG.53: 2 residues within 4Å: Chain H: D.796 Chain J: N.709 No protein-ligand interaction detected (PLIP) NAG-NAG.54: 5 residues within 4Å: Chain J: N.717, L.922, N.925, Q.926, Q.1071 2 PLIP interactions: 2 interactions with chain J Hydrophobic interactions: J:L.922, J:N.925 NAG-NAG.55: 2 residues within 4Å: Chain J: N.801, S.803 No protein-ligand interaction detected (PLIP) NAG-NAG.56: 3 residues within 4Å: Chain J: A.706, E.1072, N.1074 No protein-ligand interaction detected (PLIP) NAG-NAG.57: 4 residues within 4Å: Chain J: N.1098, T.1100, H.1101, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG.58: 1 residues within 4Å: Chain J: N.1134 No protein-ligand interaction detected (PLIP)

64 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)(Non-functional Binders)

NAG.59: 1 residues within 4Å: Chain A: N.178 Ligand excluded by PLIP NAG.60: 3 residues within 4Å: Chain A: R.198, N.202, N.496 Ligand excluded by PLIP NAG.61: 2 residues within 4Å: Chain A: G.373, N.374 Ligand excluded by PLIP NAG.62: 1 residues within 4Å: Chain A: N.388 Ligand excluded by PLIP NAG.64: 2 residues within 4Å: Chain B: K.321, N.334 Ligand excluded by PLIP NAG.66: 1 residues within 4Å: Chain C: N.178 Ligand excluded by PLIP NAG.67: 3 residues within 4Å: Chain C: R.198, N.202, N.496 Ligand excluded by PLIP NAG.68: 2 residues within 4Å: Chain C: G.373, N.374 Ligand excluded by PLIP NAG.69: 1 residues within 4Å: Chain C: N.388 Ligand excluded by PLIP NAG.71: 2 residues within 4Å: Chain D: K.321, N.334 Ligand excluded by PLIP NAG.73: 2 residues within 4Å: Chain E: Y.28, N.61 Ligand excluded by PLIP NAG.74: 3 residues within 4Å: Chain E: N.122, T.124, V.127 Ligand excluded by PLIP NAG.75: 2 residues within 4Å: Chain E: E.132, N.165 Ligand excluded by PLIP NAG.76: 4 residues within 4Å: Chain E: G.232, N.234 Chain G: E.465, R.466 Ligand excluded by PLIP NAG.77: 4 residues within 4Å: Chain E: N.280, E.281, N.282 Chain G: K.558 Ligand excluded by PLIP NAG.78: 2 residues within 4Å: Chain E: N.603, T.604 Ligand excluded by PLIP NAG.79: 1 residues within 4Å: Chain E: N.616 Ligand excluded by PLIP NAG.80: 1 residues within 4Å: Chain E: N.657 Ligand excluded by PLIP NAG.81: 3 residues within 4Å: Chain E: N.709, G.1131 Chain F: D.796 Ligand excluded by PLIP NAG.82: 2 residues within 4Å: Chain F: Y.28, N.61 Ligand excluded by PLIP NAG.83: 3 residues within 4Å: Chain F: N.122, T.124, V.127 Ligand excluded by PLIP NAG.84: 2 residues within 4Å: Chain F: E.132, N.165 Ligand excluded by PLIP NAG.85: 2 residues within 4Å: Chain F: G.232, N.234 Ligand excluded by PLIP NAG.86: 3 residues within 4Å: Chain F: N.280, E.281, N.282 Ligand excluded by PLIP NAG.87: 2 residues within 4Å: Chain F: N.603, T.604 Ligand excluded by PLIP NAG.88: 1 residues within 4Å: Chain F: N.616 Ligand excluded by PLIP NAG.89: 1 residues within 4Å: Chain F: N.657 Ligand excluded by PLIP NAG.90: 5 residues within 4Å: Chain F: A.706, E.1072, K.1073, N.1074 Ligands: NAG.91 Ligand excluded by PLIP NAG.91: 1 residues within 4Å: Ligands: NAG.90 Ligand excluded by PLIP NAG.92: 2 residues within 4Å: Chain G: Y.28, N.61 Ligand excluded by PLIP NAG.93: 3 residues within 4Å: Chain G: N.122, T.124, V.127 Ligand excluded by PLIP NAG.94: 2 residues within 4Å: Chain G: E.132, N.165 Ligand excluded by PLIP NAG.95: 2 residues within 4Å: Chain F: E.465 Chain G: N.234 Ligand excluded by PLIP NAG.96: 4 residues within 4Å: Chain F: K.558 Chain G: N.280, E.281, N.282 Ligand excluded by PLIP NAG.97: 2 residues within 4Å: Chain G: N.603, T.604 Ligand excluded by PLIP NAG.98: 1 residues within 4Å: Chain G: N.616 Ligand excluded by PLIP NAG.99: 1 residues within 4Å: Chain G: N.657 Ligand excluded by PLIP NAG.100: 2 residues within 4Å: Chain H: Y.28, N.61 Ligand excluded by PLIP NAG.101: 3 residues within 4Å: Chain H: N.122, T.124, V.127 Ligand excluded by PLIP NAG.102: 2 residues within 4Å: Chain H: E.132, N.165 Ligand excluded by PLIP NAG.103: 4 residues within 4Å: Chain H: G.232, N.234 Chain J: E.465, R.466 Ligand excluded by PLIP NAG.104: 4 residues within 4Å: Chain H: N.280, E.281, N.282 Chain J: K.558 Ligand excluded by PLIP NAG.105: 2 residues within 4Å: Chain H: N.603, T.604 Ligand excluded by PLIP NAG.106: 1 residues within 4Å: Chain H: N.616 Ligand excluded by PLIP NAG.107: 1 residues within 4Å: Chain H: N.657 Ligand excluded by PLIP NAG.108: 3 residues within 4Å: Chain H: N.709, G.1131 Chain I: D.796 Ligand excluded by PLIP NAG.109: 2 residues within 4Å: Chain I: Y.28, N.61 Ligand excluded by PLIP NAG.110: 3 residues within 4Å: Chain I: N.122, T.124, V.127 Ligand excluded by PLIP NAG.111: 2 residues within 4Å: Chain I: E.132, N.165 Ligand excluded by PLIP NAG.112: 2 residues within 4Å: Chain I: G.232, N.234 Ligand excluded by PLIP NAG.113: 3 residues within 4Å: Chain I: N.280, E.281, N.282 Ligand excluded by PLIP NAG.114: 2 residues within 4Å: Chain I: N.603, T.604 Ligand excluded by PLIP NAG.115: 1 residues within 4Å: Chain I: N.616 Ligand excluded by PLIP NAG.116: 1 residues within 4Å: Chain I: N.657 Ligand excluded by PLIP NAG.117: 5 residues within 4Å: Chain I: A.706, E.1072, K.1073, N.1074 Ligands: NAG.118 Ligand excluded by PLIP NAG.118: 1 residues within 4Å: Ligands: NAG.117 Ligand excluded by PLIP NAG.119: 2 residues within 4Å: Chain J: Y.28, N.61 Ligand excluded by PLIP NAG.120: 3 residues within 4Å: Chain J: N.122, T.124, V.127 Ligand excluded by PLIP NAG.121: 2 residues within 4Å: Chain J: E.132, N.165 Ligand excluded by PLIP NAG.122: 2 residues within 4Å: Chain I: E.465 Chain J: N.234 Ligand excluded by PLIP NAG.123: 4 residues within 4Å: Chain I: K.558 Chain J: N.280, E.281, N.282 Ligand excluded by PLIP NAG.124: 2 residues within 4Å: Chain J: N.603, T.604 Ligand excluded by PLIP NAG.125: 1 residues within 4Å: Chain J: N.616 Ligand excluded by PLIP NAG.126: 1 residues within 4Å: Chain J: N.657 Ligand excluded by PLIP

2 x LEU: LEUCINE(Non-covalent)

LEU.63: 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:F.68, A:F.297 LEU.70: 12 residues within 4Å: Chain C: 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 C, Hydrophobic interactions: C:F.68, C:Y.149, C:F.303 Hydrogen bonds: C:F.68, C:F.297

2 x ZN: ZINC ION(Non-covalent)

ZN.65: 4 residues within 4Å: Chain B: H.386, E.387, H.390, E.414 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:H.386, B:E.414 ZN.72: 4 residues within 4Å: Chain D: H.386, E.387, H.390, E.414 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:H.386, D:E.414

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yan, R. et al., Structural basis for the different states of the spike protein of SARS-CoV-2 in complex with ACE2. Cell Res. (2021)

Release Date

2021-03-31

Peptides

Sodium-dependent neutral amino acid transporter B(0)AT1: AC
Angiotensin-converting enzyme 2: BD
Spike glycoprotein: EFGHIJ

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

B
B

D
D

E
E

F
F

G
G

H
H

I
I

J
J

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 glycoprotein

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