SMTL ID : 7upw.1

Three RBD-down state of SARS-CoV-2 D614G spike in complex with the SP1-77 neutralizing antibody Fab fragment

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY 2.70 Å

Oligo State

hetero-3-3-3-mer

Ligands

6 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: 2 residues within 4Å: Chain A: N.17, N.137 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 3 residues within 4Å: Chain A: N.616, Q.644 Chain B: Q.836 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 1 residues within 4Å: Chain B: N.17 No protein-ligand interaction detected (PLIP) NAG-NAG.17: 5 residues within 4Å: Chain B: N.616, T.618, Q.644 Chain C: I.834, Q.836 No protein-ligand interaction detected (PLIP) NAG-NAG.25: 1 residues within 4Å: Chain C: N.17 No protein-ligand interaction detected (PLIP) NAG-NAG.29: 3 residues within 4Å: Chain A: Q.836 Chain C: N.616, T.618 No protein-ligand interaction detected (PLIP)

24 x NAG- NAG- MAN: alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-MAN.2: 4 residues within 4Å: Chain A: N.122, T.124, N.125, V.171 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:V.171 NAG-NAG-MAN.3: 10 residues within 4Å: Chain A: T.108, N.234, T.236 Chain C: R.457, K.458, S.459, N.460, L.461, K.462, E.465 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.4: 3 residues within 4Å: Chain A: N.280, E.281, N.282 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.6: 4 residues within 4Å: Chain A: N.717, L.922, Q.926, Q.1071 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.922 NAG-NAG-MAN.7: 3 residues within 4Å: Chain A: N.801, S.803, Q.804 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.9: 4 residues within 4Å: Chain A: N.1098, T.1100, H.1101, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.10: 1 residues within 4Å: Chain A: N.1134 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.12: 6 residues within 4Å: Chain A: E.132, N.164, N.165 Chain C: Y.351, A.352, I.468 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.14: 4 residues within 4Å: Chain B: N.122, T.124, N.125, V.171 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:V.171 NAG-NAG-MAN.15: 8 residues within 4Å: Chain A: R.457, K.458, S.459, N.460, K.462 Chain B: T.108, N.234, T.236 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.16: 3 residues within 4Å: Chain B: N.280, E.281, N.282 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.18: 4 residues within 4Å: Chain B: N.717, L.922, Q.926, Q.1071 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:L.922 NAG-NAG-MAN.19: 3 residues within 4Å: Chain B: N.801, S.803, Q.804 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.21: 4 residues within 4Å: Chain B: N.1098, T.1100, H.1101, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.22: 1 residues within 4Å: Chain B: N.1134 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.24: 7 residues within 4Å: Chain A: Y.351, I.468, T.470 Chain B: E.132, N.164, N.165 Chain D: S.55 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.26: 4 residues within 4Å: Chain C: N.122, T.124, N.125, V.171 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:V.171 NAG-NAG-MAN.27: 8 residues within 4Å: Chain B: R.457, K.458, S.459, N.460, K.462 Chain C: T.108, N.234, T.236 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.28: 3 residues within 4Å: Chain C: N.280, E.281, N.282 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.30: 4 residues within 4Å: Chain C: N.717, L.922, Q.926, Q.1071 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:L.922 NAG-NAG-MAN.31: 3 residues within 4Å: Chain C: N.801, S.803, Q.804 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.33: 4 residues within 4Å: Chain C: N.1098, T.1100, H.1101, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.34: 1 residues within 4Å: Chain C: N.1134 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.36: 6 residues within 4Å: Chain B: Y.351, I.468 Chain C: E.132, N.164, N.165 Chain F: S.55 No protein-ligand interaction detected (PLIP)

6 x NAG- NAG- FUC: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-FUC.8: 3 residues within 4Å: Chain A: A.706, E.1072, N.1074 No protein-ligand interaction detected (PLIP) NAG-NAG-FUC.11: 6 residues within 4Å: Chain A: F.338, G.339, N.343, L.368 Chain D: Y.103 Chain E: Y.49 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:Y.49, E:Y.49 NAG-NAG-FUC.20: 3 residues within 4Å: Chain B: A.706, E.1072, N.1074 No protein-ligand interaction detected (PLIP) NAG-NAG-FUC.23: 6 residues within 4Å: Chain B: F.338, G.339, N.343, L.368 Chain F: Y.103 Chain G: Y.49 2 PLIP interactions: 2 interactions with chain G Hydrogen bonds: G:Y.49, G:Y.49 NAG-NAG-FUC.32: 3 residues within 4Å: Chain C: A.706, E.1072, N.1074 No protein-ligand interaction detected (PLIP) NAG-NAG-FUC.35: 6 residues within 4Å: Chain C: F.338, G.339, N.343, V.367 Chain H: Y.103 Chain I: Y.49 2 PLIP interactions: 2 interactions with chain I Hydrogen bonds: I:Y.49, I:Y.49

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

NAG.37: 2 residues within 4Å: Chain A: Y.28, N.61 Ligand excluded by PLIP NAG.38: 3 residues within 4Å: Chain A: K.147, N.148, N.149 Ligand excluded by PLIP NAG.39: 4 residues within 4Å: Chain A: P.330, N.331, P.579, Q.580 Ligand excluded by PLIP NAG.40: 1 residues within 4Å: Chain A: N.603 Ligand excluded by PLIP NAG.41: 2 residues within 4Å: Chain A: H.655, N.657 Ligand excluded by PLIP NAG.42: 3 residues within 4Å: Chain A: N.709, G.1131 Chain B: D.796 Ligand excluded by PLIP NAG.43: 1 residues within 4Å: Chain A: N.1158 Ligand excluded by PLIP NAG.44: 1 residues within 4Å: Chain B: N.61 Ligand excluded by PLIP NAG.45: 3 residues within 4Å: Chain B: K.147, N.148, N.149 Ligand excluded by PLIP NAG.46: 2 residues within 4Å: Chain B: N.331, Q.580 Ligand excluded by PLIP NAG.47: 1 residues within 4Å: Chain B: N.603 Ligand excluded by PLIP NAG.48: 2 residues within 4Å: Chain B: H.655, N.657 Ligand excluded by PLIP NAG.49: 3 residues within 4Å: Chain B: N.709, G.1131 Chain C: D.796 Ligand excluded by PLIP NAG.50: 1 residues within 4Å: Chain B: N.1158 Ligand excluded by PLIP NAG.51: 2 residues within 4Å: Chain C: F.59, N.61 Ligand excluded by PLIP NAG.52: 4 residues within 4Å: Chain C: K.147, N.148, N.149, M.153 Ligand excluded by PLIP NAG.53: 4 residues within 4Å: Chain C: P.330, N.331, P.579, Q.580 Ligand excluded by PLIP NAG.54: 1 residues within 4Å: Chain C: N.603 Ligand excluded by PLIP NAG.55: 2 residues within 4Å: Chain C: H.655, N.657 Ligand excluded by PLIP NAG.56: 3 residues within 4Å: Chain A: D.796 Chain C: N.709, G.1131 Ligand excluded by PLIP NAG.57: 2 residues within 4Å: Chain C: N.1158, S.1161 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Luo, S. et al., An antibody from single human V H -rearranging mouse neutralizes all SARS-CoV-2 variants through BA.5 by inhibiting membrane fusion. Sci Immunol (2022)

Release Date

2022-08-10

Peptides

Spike glycoprotein: ABC
SP1-77 Fab heavy chain: DFH
SP1-77 Fab light chain: EGI

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

F
F

H
H

E
E

G
G

I
L

Spike glycoprotein

SP1-77 Fab heavy chain

SP1-77 Fab light chain

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