SMTL ID : 7edj.1

Cryo-EM structure of SARS-CoV-2 S-UK variant (B.1.1.7) in complex with Angiotensin-converting enzyme 2 (ACE2) ectodomain

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-mer

Ligands

29 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: 4 residues within 4Å: Chain A: N.283, E.284, N.285 Chain C: K.561 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 3 residues within 4Å: Chain A: N.334, Q.583, T.584 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.584, A:T.584 NAG-NAG.3: 4 residues within 4Å: Chain A: F.341, G.342, F.345, N.346 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 3 residues within 4Å: Chain A: N.619, T.621, Q.647 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 3 residues within 4Å: Chain A: N.712, N.713 Chain B: D.799 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 3 residues within 4Å: Chain A: N.720, Q.929, Q.1074 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 3 residues within 4Å: Chain A: N.804, S.806, Q.807 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 4 residues within 4Å: Chain A: S.707, A.709, E.1075, N.1077 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.707, A:A.709 NAG-NAG.9: 4 residues within 4Å: Chain A: N.1101, T.1103, H.1104, F.1106 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 1 residues within 4Å: Chain A: N.1137 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 4 residues within 4Å: Chain B: N.126, T.128, N.129, V.131 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 3 residues within 4Å: Chain A: K.561 Chain B: E.284, N.285 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 2 residues within 4Å: Chain B: N.334, Q.583 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 3 residues within 4Å: Chain B: N.619 Chain C: R.850, I.853 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 2 residues within 4Å: Chain B: N.712 Chain C: D.799 No protein-ligand interaction detected (PLIP) NAG-NAG.16: 1 residues within 4Å: Chain B: N.720 No protein-ligand interaction detected (PLIP) NAG-NAG.17: 1 residues within 4Å: Chain B: N.804 No protein-ligand interaction detected (PLIP) NAG-NAG.18: 3 residues within 4Å: Chain B: S.707, A.709, N.1077 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:A.709 NAG-NAG.19: 3 residues within 4Å: Chain B: N.1101, H.1104, F.1106 No protein-ligand interaction detected (PLIP) NAG-NAG.20: 1 residues within 4Å: Chain B: N.1137 No protein-ligand interaction detected (PLIP) NAG-NAG.21: 3 residues within 4Å: Chain C: N.283, E.284, N.285 No protein-ligand interaction detected (PLIP) NAG-NAG.22: 3 residues within 4Å: Chain C: N.334, Q.583, T.584 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:Q.583 Hydrogen bonds: C:T.584 NAG-NAG.23: 5 residues within 4Å: Chain A: D.851, L.852, I.853 Chain C: N.619, Q.647 No protein-ligand interaction detected (PLIP) NAG-NAG.24: 4 residues within 4Å: Chain A: D.799 Chain C: N.712, I.1133, G.1134 No protein-ligand interaction detected (PLIP) NAG-NAG.25: 2 residues within 4Å: Chain C: N.720, Q.1074 No protein-ligand interaction detected (PLIP) NAG-NAG.26: 3 residues within 4Å: Chain C: N.804, S.806, Q.807 No protein-ligand interaction detected (PLIP) NAG-NAG.27: 3 residues within 4Å: Chain C: S.707, A.709, N.1077 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:A.709 NAG-NAG.28: 3 residues within 4Å: Chain C: N.1101, H.1104, F.1106 No protein-ligand interaction detected (PLIP) NAG-NAG.29: 1 residues within 4Å: Chain C: N.1137 No protein-ligand interaction detected (PLIP)

26 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)(Non-covalent)

NAG.30: 3 residues within 4Å: Chain A: Y.34, F.65, N.67 Ligand excluded by PLIP NAG.31: 4 residues within 4Å: Chain A: N.126, A.127, T.128, N.129 Ligand excluded by PLIP NAG.32: 1 residues within 4Å: Chain A: N.168 Ligand excluded by PLIP NAG.33: 3 residues within 4Å: Chain A: G.235, I.236, N.237 Ligand excluded by PLIP NAG.34: 1 residues within 4Å: Chain A: N.606 Ligand excluded by PLIP NAG.35: 1 residues within 4Å: Chain A: N.660 Ligand excluded by PLIP NAG.36: 5 residues within 4Å: Chain B: Y.34, N.36, F.65, S.66, N.67 Ligand excluded by PLIP NAG.37: 2 residues within 4Å: Chain B: N.167, N.168 Ligand excluded by PLIP NAG.38: 3 residues within 4Å: Chain B: T.112, N.237, T.239 Ligand excluded by PLIP NAG.39: 6 residues within 4Å: Chain B: F.341, G.342, F.345, N.346, L.371, S.374 Ligand excluded by PLIP NAG.40: 1 residues within 4Å: Chain B: N.606 Ligand excluded by PLIP NAG.41: 2 residues within 4Å: Chain B: H.658, N.660 Ligand excluded by PLIP NAG.42: 3 residues within 4Å: Chain C: N.36, F.65, N.67 Ligand excluded by PLIP NAG.43: 3 residues within 4Å: Chain C: N.126, A.127, N.129 Ligand excluded by PLIP NAG.44: 1 residues within 4Å: Chain C: N.168 Ligand excluded by PLIP NAG.45: 2 residues within 4Å: Chain C: I.236, N.237 Ligand excluded by PLIP NAG.46: 5 residues within 4Å: Chain C: F.345, N.346, S.374, S.376, F.377 Ligand excluded by PLIP NAG.47: 1 residues within 4Å: Chain C: N.606 Ligand excluded by PLIP NAG.48: 2 residues within 4Å: Chain C: H.658, N.660 Ligand excluded by PLIP NAG.49: 4 residues within 4Å: Chain D: N.53, T.55, E.57, Q.340 Ligand excluded by PLIP NAG.50: 3 residues within 4Å: Chain D: N.90, L.91, T.92 Ligand excluded by PLIP NAG.51: 4 residues within 4Å: Chain D: Q.101, Q.102, N.103, N.194 Ligand excluded by PLIP NAG.52: 1 residues within 4Å: Chain D: N.322 Ligand excluded by PLIP NAG.53: 2 residues within 4Å: Chain D: D.431, N.432 Ligand excluded by PLIP NAG.54: 5 residues within 4Å: Chain D: K.416, H.417, S.420, S.545, N.546 Ligand excluded by PLIP NAG.55: 4 residues within 4Å: Chain E: N.53, T.55, E.57, N.58 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yang, T.J. et al., Effect of SARS-CoV-2 B.1.1.7 mutations on spike protein structure and function. Nat.Struct.Mol.Biol. (2021)

Release Date

2021-09-01

Peptides

Spike glycoprotein: ABC
Angiotensin-converting enzyme 2 (ACE2) ectodomain: DEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
I

E
J

F
K

Spike glycoprotein

Angiotensin-converting enzyme 2 (ACE2) ectodomain

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