SMTL ID : 7laa.1

Structure of SARS-CoV-2 S protein in complex with Receptor Binding Domain antibody DH1041

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-1-1-mer

Ligands

11 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.256 Chain E: K.532 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 4 residues within 4Å: Chain A: N.683, N.684, I.1104, G.1105 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 8 residues within 4Å: Chain A: T.690, N.691, F.692, T.693, L.896, N.899, Q.900, Q.1045 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.896 NAG-NAG.4: 5 residues within 4Å: Chain A: K.769, N.775, S.777, Q.778, Q.909 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 8 residues within 4Å: Chain A: S.678, V.679, A.680, A.687, E.1046, K.1047, N.1048 Chain B: Q.869 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.678 NAG-NAG.8: 4 residues within 4Å: Chain A: K.532 Chain B: N.254, E.255, N.256 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 7 residues within 4Å: Chain B: S.678, A.680, A.687, E.1046, K.1047, N.1048 Chain E: Q.869 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.678 NAG-NAG.12: 3 residues within 4Å: Chain B: I.1106, V.1107, N.1108 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 4 residues within 4Å: Chain E: N.254, N.256, T.258, T.260 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 8 residues within 4Å: Chain A: P.766, Q.869 Chain E: S.678, A.680, A.687, E.1046, K.1047, N.1048 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:S.678 NAG-NAG.17: 3 residues within 4Å: Chain E: I.1106, V.1107, N.1108 No protein-ligand interaction detected (PLIP)

6 x NAG- NAG- BMA: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA.6: 4 residues within 4Å: Chain A: N.1072, T.1074, H.1075, F.1077 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.7: 4 residues within 4Å: Chain A: C.1100, D.1101, V.1107, N.1108 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.9: 7 residues within 4Å: Chain B: N.691, F.692, T.693, L.896, N.899, Q.900, Q.1045 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:L.896 NAG-NAG-BMA.11: 5 residues within 4Å: Chain B: N.1072, G.1073, T.1074, H.1075, F.1077 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:H.1075 NAG-NAG-BMA.14: 9 residues within 4Å: Chain E: T.690, N.691, F.692, T.693, L.896, N.899, Q.900, Q.1045, F.1083 1 PLIP interactions: 1 interactions with chain E Hydrophobic interactions: E:L.896 NAG-NAG-BMA.16: 5 residues within 4Å: Chain E: N.1072, G.1073, T.1074, H.1075, F.1077 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:H.1075

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

NAG.18: 4 residues within 4Å: Chain A: N.96, T.98, N.99, V.101 Ligand excluded by PLIP NAG.19: 3 residues within 4Å: Chain A: N.305, Q.554, T.555 Ligand excluded by PLIP NAG.20: 8 residues within 4Å: Chain A: G.313, F.316, N.317, V.341, L.342, S.345, S.347, F.348 Ligand excluded by PLIP NAG.21: 2 residues within 4Å: Chain A: N.590, T.592 Ligand excluded by PLIP NAG.22: 3 residues within 4Å: Chain A: H.629, V.630, N.631 Ligand excluded by PLIP NAG.23: 4 residues within 4Å: Chain B: Y.2, N.4, F.33, N.35 Ligand excluded by PLIP NAG.24: 6 residues within 4Å: Chain B: V.94, N.96, T.98, N.99, V.101, V.145 Ligand excluded by PLIP NAG.25: 4 residues within 4Å: Chain A: E.439 Chain B: T.82, N.208, T.210 Ligand excluded by PLIP NAG.26: 2 residues within 4Å: Chain B: N.590, T.592 Ligand excluded by PLIP NAG.27: 4 residues within 4Å: Chain B: N.683, N.684, I.1104, G.1105 Ligand excluded by PLIP NAG.28: 4 residues within 4Å: Chain B: N.775, S.777, Q.778, Q.909 Ligand excluded by PLIP NAG.29: 5 residues within 4Å: Chain E: Y.2, N.4, F.33, S.34, N.35 Ligand excluded by PLIP NAG.30: 4 residues within 4Å: Chain E: N.96, A.97, T.98, N.99 Ligand excluded by PLIP NAG.31: 4 residues within 4Å: Chain E: T.82, N.208, I.209, T.210 Ligand excluded by PLIP NAG.32: 4 residues within 4Å: Chain E: N.590, C.591, T.592, Q.618 Ligand excluded by PLIP NAG.33: 4 residues within 4Å: Chain E: N.683, N.684, I.1104, G.1105 Ligand excluded by PLIP NAG.34: 3 residues within 4Å: Chain E: N.775, S.777, Q.778 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

2021-03-17

Peptides

Spike glycoprotein: ABE
DH1041 heavy chain: C
DH1041 light chain: D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

E
C

C
H

D
L

Spike glycoprotein

DH1041 heavy chain

DH1041 light chain

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