SMTL ID : 7ld1.1

Structure of SARS-CoV-2 S protein in complex with Receptor Binding Domain antibody DH1047

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 3.40 Å

Oligo State

hetero-3-3-3-mer

Ligands

13 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.1: 5 residues within 4Å: Chain A: S.1071, N.1072, T.1074, H.1075, F.1077 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.3: 3 residues within 4Å: Chain A: N.305, Q.554, L.556 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.4: 5 residues within 4Å: Chain A: F.312, G.313, F.316, N.317, S.347 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:S.347 NAG-NAG-BMA.5: 3 residues within 4Å: Chain A: N.691, L.896, Q.1045 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.6: 1 residues within 4Å: Chain A: N.1108 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.7: 2 residues within 4Å: Chain B: I.1106, N.1108 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.9: 2 residues within 4Å: Chain B: N.305, Q.554 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.10: 4 residues within 4Å: Chain B: F.312, G.313, F.316, N.317 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.11: 3 residues within 4Å: Chain B: N.691, L.896, Q.1045 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.12: 3 residues within 4Å: Chain C: N.305, P.553, Q.554 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.13: 4 residues within 4Å: Chain C: H.1057, I.1106, V.1107, N.1108 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.14: 2 residues within 4Å: Chain C: G.313, N.317 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.15: 3 residues within 4Å: Chain C: N.691, L.896, Q.1045 No protein-ligand interaction detected (PLIP)

2 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.2: 1 residues within 4Å: Chain A: N.256 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 3 residues within 4Å: Chain A: K.532 Chain B: N.254, N.256 No protein-ligand interaction detected (PLIP)

24 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)(Non-covalent)

NAG.16: 2 residues within 4Å: Chain A: N.683, G.1105 Ligand excluded by PLIP NAG.17: 2 residues within 4Å: Chain A: E.1046, N.1048 Ligand excluded by PLIP NAG.18: 2 residues within 4Å: Chain A: Y.2, N.35 Ligand excluded by PLIP NAG.19: 1 residues within 4Å: Chain A: N.208 Ligand excluded by PLIP NAG.20: 2 residues within 4Å: Chain A: N.577, T.578 Ligand excluded by PLIP NAG.21: 2 residues within 4Å: Chain A: N.590, T.592 Ligand excluded by PLIP NAG.22: 1 residues within 4Å: Chain A: N.631 Ligand excluded by PLIP NAG.23: 2 residues within 4Å: Chain A: N.138, N.139 Ligand excluded by PLIP NAG.24: 2 residues within 4Å: Chain B: N.590, T.592 Ligand excluded by PLIP NAG.25: 1 residues within 4Å: Chain B: N.683 Ligand excluded by PLIP NAG.26: 2 residues within 4Å: Chain B: A.680, N.1048 Ligand excluded by PLIP NAG.27: 2 residues within 4Å: Chain B: Y.2, N.35 Ligand excluded by PLIP NAG.28: 3 residues within 4Å: Chain B: N.96, A.97, T.98 Ligand excluded by PLIP NAG.29: 3 residues within 4Å: Chain B: G.206, I.207, N.208 Ligand excluded by PLIP NAG.30: 1 residues within 4Å: Chain B: N.577 Ligand excluded by PLIP NAG.31: 2 residues within 4Å: Chain B: H.629, N.631 Ligand excluded by PLIP NAG.32: 2 residues within 4Å: Chain B: Q.89, N.139 Ligand excluded by PLIP NAG.33: 4 residues within 4Å: Chain C: Q.89, N.139, C.140, T.141 Ligand excluded by PLIP NAG.34: 1 residues within 4Å: Chain C: N.631 Ligand excluded by PLIP NAG.35: 3 residues within 4Å: Chain C: N.96, T.98, V.101 Ligand excluded by PLIP NAG.36: 2 residues within 4Å: Chain C: Y.2, N.35 Ligand excluded by PLIP NAG.37: 2 residues within 4Å: Chain C: N.590, T.592 Ligand excluded by PLIP NAG.38: 1 residues within 4Å: Chain C: N.683 Ligand excluded by PLIP NAG.39: 2 residues within 4Å: Chain C: A.680, N.1048 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: ABC
DH1047 heavy chain: DFH
DH1047 light chain: EGI

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
M

F
P

H
H

E
N

G
O

I
L

Spike glycoprotein

DH1047 heavy chain

DH1047 light chain

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