SMTL ID : 7sg4.1

Structure of SARS-CoV S protein in complex with Receptor Binding Domain antibody DH1047

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-1-1-mer

Ligands

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

NAG.1: 4 residues within 4Å: Chain A: S.35, N.65, V.66, H.70 Ligand excluded by PLIP NAG.2: 4 residues within 4Å: Chain A: N.108, N.109, E.131, C.133 Ligand excluded by PLIP NAG.3: 7 residues within 4Å: Chain A: C.1064, H.1065, E.1066, G.1067, N.1116, N.1117, T.1118 Ligand excluded by PLIP NAG.4: 3 residues within 4Å: Chain A: N.1080, T.1082, F.1085 Ligand excluded by PLIP NAG.5: 4 residues within 4Å: Chain A: T.693, N.1056, F.1057, T.1058 Ligand excluded by PLIP NAG.6: 4 residues within 4Å: Chain A: Y.778, N.783, S.785, Q.786 Ligand excluded by PLIP NAG.7: 3 residues within 4Å: Chain A: N.699, Q.904, Q.1053 Ligand excluded by PLIP NAG.8: 1 residues within 4Å: Chain A: N.691 Ligand excluded by PLIP NAG.9: 2 residues within 4Å: Chain A: N.602, T.604 Ligand excluded by PLIP NAG.10: 3 residues within 4Å: Chain A: N.589, A.590, E.821 Ligand excluded by PLIP NAG.11: 1 residues within 4Å: Chain A: N.357 Ligand excluded by PLIP NAG.12: 9 residues within 4Å: Chain A: F.329, N.330, A.331, L.355, S.358, F.360, F.361, W.423, R.495 Ligand excluded by PLIP NAG.13: 2 residues within 4Å: Chain A: N.318, K.566 Ligand excluded by PLIP NAG.14: 3 residues within 4Å: Chain A: E.268, N.269 Chain C: R.544 Ligand excluded by PLIP NAG.15: 3 residues within 4Å: Chain A: S.105, N.227, T.229 Ligand excluded by PLIP NAG.16: 3 residues within 4Å: Chain A: N.129, F.157, N.158 Ligand excluded by PLIP NAG.17: 4 residues within 4Å: Chain B: S.35, N.65, V.66, D.208 Ligand excluded by PLIP NAG.18: 5 residues within 4Å: Chain B: N.109, Q.112, N.129, F.157, N.158 Ligand excluded by PLIP NAG.19: 3 residues within 4Å: Chain B: H.1065, N.1116, N.1117 Ligand excluded by PLIP NAG.20: 4 residues within 4Å: Chain B: N.1080, T.1082, S.1083, F.1085 Ligand excluded by PLIP NAG.21: 1 residues within 4Å: Chain B: N.1056 Ligand excluded by PLIP NAG.22: 4 residues within 4Å: Chain B: Y.778, N.783, S.785, Q.786 Ligand excluded by PLIP NAG.23: 3 residues within 4Å: Chain B: N.699, Q.904, Q.1053 Ligand excluded by PLIP NAG.24: 1 residues within 4Å: Chain B: N.691 Ligand excluded by PLIP NAG.25: 2 residues within 4Å: Chain B: N.602, T.604 Ligand excluded by PLIP NAG.26: 3 residues within 4Å: Chain B: N.589, Y.819, E.821 Ligand excluded by PLIP NAG.27: 6 residues within 4Å: Chain B: S.353, Y.356, N.357, T.372, N.375, D.376 Ligand excluded by PLIP NAG.28: 8 residues within 4Å: Chain B: F.329, N.330, S.358, F.360, F.361, W.423, R.495, V.497 Ligand excluded by PLIP NAG.29: 3 residues within 4Å: Chain B: N.318, P.565, K.566 Ligand excluded by PLIP NAG.30: 3 residues within 4Å: Chain A: R.544 Chain B: E.268, N.269 Ligand excluded by PLIP NAG.31: 3 residues within 4Å: Chain B: S.105, N.227, T.229 Ligand excluded by PLIP NAG.32: 2 residues within 4Å: Chain C: N.65, V.66 Ligand excluded by PLIP NAG.33: 4 residues within 4Å: Chain C: N.109, N.129, E.131, F.157 Ligand excluded by PLIP NAG.34: 8 residues within 4Å: Chain C: C.1064, H.1065, E.1066, G.1067, C.1108, N.1116, N.1117, T.1118 Ligand excluded by PLIP NAG.35: 4 residues within 4Å: Chain C: N.1080, T.1082, S.1083, F.1085 Ligand excluded by PLIP NAG.36: 1 residues within 4Å: Chain C: N.1056 Ligand excluded by PLIP NAG.37: 4 residues within 4Å: Chain C: Y.778, N.783, S.785, Q.786 Ligand excluded by PLIP NAG.38: 3 residues within 4Å: Chain C: N.699, Q.904, Q.1053 Ligand excluded by PLIP NAG.39: 2 residues within 4Å: Chain C: N.691, G.1113 Ligand excluded by PLIP NAG.40: 2 residues within 4Å: Chain C: N.602, T.604 Ligand excluded by PLIP NAG.41: 3 residues within 4Å: Chain C: N.589, Y.819, E.821 Ligand excluded by PLIP NAG.42: 5 residues within 4Å: Chain C: S.353, Y.356, N.357, T.359, N.375 Ligand excluded by PLIP NAG.43: 9 residues within 4Å: Chain C: F.329, N.330, F.334, S.358, F.360, F.361, W.423, R.495, V.497 Ligand excluded by PLIP NAG.44: 4 residues within 4Å: Chain C: N.318, I.319, K.566, T.567 Ligand excluded by PLIP NAG.45: 3 residues within 4Å: Chain B: R.544 Chain C: E.268, N.269 Ligand excluded by PLIP NAG.46: 5 residues within 4Å: Chain C: N.189, G.192, G.225, I.226, N.227 Ligand excluded by PLIP NAG.47: 5 residues within 4Å: Chain C: K.110, S.111, Q.112, N.129, N.158 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Martinez, D.R. et al., A broadly cross-reactive antibody neutralizes and protects against sarbecovirus challenge in mice. Sci Transl Med (2022)

Release Date

2021-11-10

Peptides

Spike glycoprotein: ABC
DH1047 Heavy chain: D
DH1047 light chain: E

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
H

E
L

Spike glycoprotein

DH1047 Heavy chain

DH1047 light chain

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