SMTL ID : 7lab.1

Structure of SARS-CoV-2 S protein in complex with N-terminal domain antibody DH1052

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY 2.97 Å

Oligo State

hetero-3-3-3-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)(Non-covalent)

NAG-NAG.1: 3 residues within 4Å: Chain E: I.1106, V.1107, N.1108 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 5 residues within 4Å: Chain F: N.1072, G.1073, T.1074, H.1075, F.1077 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 4 residues within 4Å: Chain E: E.439 Chain F: T.82, N.208, T.210 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 1 residues within 4Å: Chain F: N.1108 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 7 residues within 4Å: Chain F: T.690, N.691, T.693, L.896, N.899, Q.900, Q.1045 3 PLIP interactions: 3 interactions with chain F Hydrophobic interactions: F:L.896, F:N.899, F:Q.900 NAG-NAG.6: 3 residues within 4Å: Chain F: N.775, S.777, Q.778 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 6 residues within 4Å: Chain G: T.690, N.691, L.896, N.899, Q.900, Q.1045 2 PLIP interactions: 2 interactions with chain G Hydrophobic interactions: G:L.896, G:N.899 NAG-NAG.8: 3 residues within 4Å: Chain G: N.775, S.777, Q.778 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 2 residues within 4Å: Chain G: V.1107, N.1108 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 6 residues within 4Å: Chain E: T.82, N.208, T.210, R.211 Chain G: K.436, E.439 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 6 residues within 4Å: Chain E: N.691, F.692, L.896, N.899, Q.900, Q.1045 2 PLIP interactions: 2 interactions with chain E Hydrophobic interactions: E:L.896, E:Q.900 NAG-NAG.12: 4 residues within 4Å: Chain E: N.775, S.777, Q.778, Q.909 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 5 residues within 4Å: Chain E: N.1072, G.1073, T.1074, H.1075, F.1077 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 5 residues within 4Å: Chain G: N.1072, G.1073, T.1074, H.1075, F.1077 No protein-ligand interaction detected (PLIP)

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

NAG.15: 3 residues within 4Å: Chain D: G.109 Chain E: Y.2, N.35 Ligand excluded by PLIP NAG.16: 8 residues within 4Å: Chain E: L.92, V.94, N.96, A.97, T.98, N.99, V.101, K.103 Ligand excluded by PLIP NAG.17: 4 residues within 4Å: Chain E: N.254, N.256, T.260 Chain G: K.532 Ligand excluded by PLIP NAG.18: 5 residues within 4Å: Chain E: P.304, N.305, P.553, Q.554, L.556 Ligand excluded by PLIP NAG.19: 6 residues within 4Å: Chain E: G.313, F.316, N.317, V.341, L.342, F.348 Ligand excluded by PLIP NAG.20: 2 residues within 4Å: Chain E: N.577, T.578 Ligand excluded by PLIP NAG.21: 4 residues within 4Å: Chain E: N.590, T.592, Q.618, R.620 Ligand excluded by PLIP NAG.22: 1 residues within 4Å: Chain E: N.631 Ligand excluded by PLIP NAG.23: 4 residues within 4Å: Chain E: N.683, N.684, I.1104, G.1105 Ligand excluded by PLIP NAG.24: 6 residues within 4Å: Chain E: A.680, A.687, E.1046, K.1047, N.1048 Chain F: Q.869 Ligand excluded by PLIP NAG.25: 3 residues within 4Å: Chain E: S.86, E.106, N.139 Ligand excluded by PLIP NAG.26: 3 residues within 4Å: Chain F: N.254, E.255, N.256 Ligand excluded by PLIP NAG.27: 5 residues within 4Å: Chain F: N.305, P.553, Q.554, T.555, L.556 Ligand excluded by PLIP NAG.28: 5 residues within 4Å: Chain F: F.312, G.313, F.316, N.317, L.342 Ligand excluded by PLIP NAG.29: 3 residues within 4Å: Chain F: N.577, T.578, A.916 Ligand excluded by PLIP NAG.30: 3 residues within 4Å: Chain F: N.590, T.592, Q.618 Ligand excluded by PLIP NAG.31: 1 residues within 4Å: Chain F: N.631 Ligand excluded by PLIP NAG.32: 5 residues within 4Å: Chain F: N.683, N.684, P.1053, I.1104, G.1105 Ligand excluded by PLIP NAG.33: 4 residues within 4Å: Chain F: A.680, E.1046, N.1048 Chain G: Q.869 Ligand excluded by PLIP NAG.34: 5 residues within 4Å: Chain F: Y.2, N.4, F.33, S.34, N.35 Ligand excluded by PLIP NAG.35: 6 residues within 4Å: Chain G: Y.2, F.33, S.34, N.35 Chain H: G.109, S.110 Ligand excluded by PLIP NAG.36: 4 residues within 4Å: Chain G: N.96, A.97, N.99, V.101 Ligand excluded by PLIP NAG.37: 4 residues within 4Å: Chain F: K.532 Chain G: N.254, N.256, T.260 Ligand excluded by PLIP NAG.38: 5 residues within 4Å: Chain G: N.305, P.553, Q.554, T.555, L.556 Ligand excluded by PLIP NAG.39: 7 residues within 4Å: Chain G: F.312, G.313, F.316, N.317, V.341, L.342, F.348 Ligand excluded by PLIP NAG.40: 2 residues within 4Å: Chain G: N.577, T.578 Ligand excluded by PLIP NAG.41: 3 residues within 4Å: Chain G: N.590, T.592, Q.618 Ligand excluded by PLIP NAG.42: 3 residues within 4Å: Chain G: H.629, V.630, N.631 Ligand excluded by PLIP NAG.43: 5 residues within 4Å: Chain G: N.683, N.684, P.1053, I.1104, G.1105 Ligand excluded by PLIP NAG.44: 6 residues within 4Å: Chain E: Q.869 Chain G: A.680, A.687, E.1046, K.1047, N.1048 Ligand excluded by PLIP NAG.45: 3 residues within 4Å: Chain G: S.86, E.106, N.139 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Li, D. et al., In vitro and in vivo functions of SARS-CoV-2 infection-enhancing and neutralizing antibodies. Cell (2021)

Release Date

2021-03-10

Peptides

DH1052 light chain: ACI
DH1052 heavy chain: BDH
Spike glycoprotein: EFG

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
X

C
S

I
L

B
Y

D
T

H
H

E
A

F
B

G
C

DH1052 light chain

DH1052 heavy chain

Spike glycoprotein

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