SMTL ID : 7lcn.1

Structure of SARS-CoV-2 S protein in complex with N-terminal domain antibody DH1050.1

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY 3.35 Å

Oligo State

hetero-3-3-3-mer

Ligands

15 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: 5 residues within 4Å: Chain A: T.82, N.208, T.210 Chain D: E.439, R.440 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 5 residues within 4Å: Chain A: N.691, F.692, L.896, Q.900, Q.1045 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 4 residues within 4Å: Chain A: N.775, S.777, Q.778, F.791 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 6 residues within 4Å: Chain A: N.1072, G.1073, T.1074, H.1075, F.1077, I.1088 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.1075 NAG-NAG.5: 3 residues within 4Å: Chain A: I.1106, V.1107, N.1108 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 4 residues within 4Å: Chain D: T.82, T.83, N.208, T.210 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 6 residues within 4Å: Chain D: N.691, F.692, L.896, N.899, Q.900, Q.1045 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 4 residues within 4Å: Chain D: N.775, S.777, Q.778, F.791 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:F.791 NAG-NAG.9: 5 residues within 4Å: Chain D: N.1072, G.1073, T.1074, H.1075, F.1077 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:H.1075 NAG-NAG.10: 3 residues within 4Å: Chain D: I.1106, V.1107, N.1108 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 5 residues within 4Å: Chain G: T.82, T.83, N.208, T.210, R.211 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 6 residues within 4Å: Chain G: N.691, F.692, L.896, N.899, Q.900, Q.1045 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 4 residues within 4Å: Chain G: N.775, S.777, Q.778, F.791 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 6 residues within 4Å: Chain G: N.1072, G.1073, T.1074, H.1075, F.1077, I.1088 1 PLIP interactions: 1 interactions with chain G Hydrogen bonds: G:H.1075 NAG-NAG.15: 3 residues within 4Å: Chain G: I.1106, V.1107, N.1108 No protein-ligand interaction detected (PLIP)

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

NAG.16: 2 residues within 4Å: Chain A: Y.2, N.35 Ligand excluded by PLIP NAG.17: 6 residues within 4Å: Chain A: N.96, A.97, T.98, N.99, V.101, K.103 Ligand excluded by PLIP NAG.18: 4 residues within 4Å: Chain A: N.254, E.255, N.256 Chain D: K.532 Ligand excluded by PLIP NAG.19: 5 residues within 4Å: Chain A: N.305, P.553, Q.554, T.555, L.556 Ligand excluded by PLIP NAG.20: 6 residues within 4Å: Chain A: F.312, G.313, F.316, N.317, V.341, L.342 Ligand excluded by PLIP NAG.21: 1 residues within 4Å: Chain A: N.577 Ligand excluded by PLIP NAG.22: 4 residues within 4Å: Chain A: N.590, T.592, E.593, Q.618 Ligand excluded by PLIP NAG.23: 3 residues within 4Å: Chain A: H.629, V.630, N.631 Ligand excluded by PLIP NAG.24: 5 residues within 4Å: Chain A: N.683, N.684, G.1105 Chain G: I.768, D.770 Ligand excluded by PLIP NAG.25: 5 residues within 4Å: Chain A: A.680, A.687, E.1046, N.1048 Chain G: Q.869 Ligand excluded by PLIP NAG.26: 4 residues within 4Å: Chain A: E.106, A.137, N.138, N.139 Ligand excluded by PLIP NAG.27: 4 residues within 4Å: Chain D: Y.2, T.3, N.4, N.35 Ligand excluded by PLIP NAG.28: 6 residues within 4Å: Chain D: N.96, A.97, T.98, N.99, V.101, K.103 Ligand excluded by PLIP NAG.29: 4 residues within 4Å: Chain D: N.254, E.255, N.256 Chain G: K.532 Ligand excluded by PLIP NAG.30: 4 residues within 4Å: Chain D: N.305, P.553, Q.554, L.556 Ligand excluded by PLIP NAG.31: 6 residues within 4Å: Chain D: F.312, G.313, F.316, N.317, L.342, F.348 Ligand excluded by PLIP NAG.32: 2 residues within 4Å: Chain D: N.577, T.578 Ligand excluded by PLIP NAG.33: 3 residues within 4Å: Chain D: N.590, T.592, E.593 Ligand excluded by PLIP NAG.34: 3 residues within 4Å: Chain D: H.629, V.630, N.631 Ligand excluded by PLIP NAG.35: 5 residues within 4Å: Chain A: I.768, D.770 Chain D: N.683, N.684, G.1105 Ligand excluded by PLIP NAG.36: 5 residues within 4Å: Chain A: Q.869 Chain D: A.680, A.687, E.1046, N.1048 Ligand excluded by PLIP NAG.37: 4 residues within 4Å: Chain D: E.106, A.137, N.138, N.139 Ligand excluded by PLIP NAG.38: 4 residues within 4Å: Chain G: Y.2, T.3, N.4, N.35 Ligand excluded by PLIP NAG.39: 8 residues within 4Å: Chain G: N.96, A.97, T.98, N.99, V.100, V.101, V.145, S.146 Ligand excluded by PLIP NAG.40: 4 residues within 4Å: Chain A: K.532 Chain G: N.254, E.255, N.256 Ligand excluded by PLIP NAG.41: 4 residues within 4Å: Chain G: N.305, P.553, Q.554, L.556 Ligand excluded by PLIP NAG.42: 6 residues within 4Å: Chain G: F.312, G.313, F.316, N.317, L.342, F.348 Ligand excluded by PLIP NAG.43: 2 residues within 4Å: Chain G: N.577, T.578 Ligand excluded by PLIP NAG.44: 3 residues within 4Å: Chain G: N.590, T.592, Q.618 Ligand excluded by PLIP NAG.45: 3 residues within 4Å: Chain G: H.629, V.630, N.631 Ligand excluded by PLIP NAG.46: 5 residues within 4Å: Chain D: I.768, D.770 Chain G: N.683, N.684, G.1105 Ligand excluded by PLIP NAG.47: 5 residues within 4Å: Chain D: Q.869 Chain G: A.680, A.687, E.1046, N.1048 Ligand excluded by PLIP NAG.48: 4 residues within 4Å: Chain G: E.106, A.137, N.138, 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

2021-01-27

Peptides

Spike glycoprotein: ADG
DH1050.1 heavy chain: BEH
DH1050.1 light chain: CFI

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

D
A

G
K

B
H

E
B

H
M

C
L

F
D

I
S

Spike glycoprotein

DH1050.1 heavy chain

DH1050.1 light chain

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