SMTL ID : 8hlc.1

S protein of SARS-CoV-2 in complex with 3711

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-3-mer

Ligands

23 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: C.15, N.17, N.137 Chain E: N.50, G.85 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 8 residues within 4Å: Chain A: N.164, N.165 Chain C: Y.351, L.452, I.468, T.470, L.492 Chain E: S.75 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:L.452, C:L.492 NAG-NAG.4: 8 residues within 4Å: Chain A: T.108, N.234, T.236 Chain C: R.457, S.459, N.460, K.462, E.465 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:S.459 NAG-NAG.5: 1 residues within 4Å: Chain A: N.282 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 1 residues within 4Å: Chain A: N.331 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 3 residues within 4Å: Chain A: G.339, N.343, N.370 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.370 NAG-NAG.8: 4 residues within 4Å: Chain A: N.717, L.922, Q.926, Q.1071 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.922 NAG-NAG.9: 3 residues within 4Å: Chain A: A.706, E.1072, N.1074 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 4 residues within 4Å: Chain A: N.1098, T.1100, H.1101, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 5 residues within 4Å: Chain B: C.15, N.17, N.137 Chain G: N.50, G.85 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 7 residues within 4Å: Chain A: Y.351, L.452, I.468, L.492 Chain B: N.164, N.165 Chain G: S.75 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:Y.351, A:L.452, A:L.492 NAG-NAG.14: 8 residues within 4Å: Chain A: R.457, S.459, N.460, K.462, E.465 Chain B: T.108, N.234, T.236 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.459 NAG-NAG.15: 1 residues within 4Å: Chain B: N.282 No protein-ligand interaction detected (PLIP) NAG-NAG.16: 1 residues within 4Å: Chain B: N.331 No protein-ligand interaction detected (PLIP) NAG-NAG.17: 4 residues within 4Å: Chain B: N.717, L.922, Q.926, Q.1071 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:L.922 NAG-NAG.18: 4 residues within 4Å: Chain B: N.1098, T.1100, H.1101, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG.19: 5 residues within 4Å: Chain C: C.15, N.17, N.137 Chain I: N.50, G.85 No protein-ligand interaction detected (PLIP) NAG-NAG.21: 7 residues within 4Å: Chain B: Y.351, L.452, I.468, L.492 Chain C: N.164, N.165 Chain I: S.75 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:Y.351, B:L.452, B:L.492 Hydrogen bonds: B:Y.351 NAG-NAG.22: 6 residues within 4Å: Chain B: S.459, K.462, E.465 Chain C: T.108, N.234, T.236 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.459 NAG-NAG.23: 1 residues within 4Å: Chain C: N.282 No protein-ligand interaction detected (PLIP) NAG-NAG.24: 1 residues within 4Å: Chain C: N.331 No protein-ligand interaction detected (PLIP) NAG-NAG.25: 4 residues within 4Å: Chain C: N.717, L.922, Q.926, Q.1071 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:L.922 NAG-NAG.26: 4 residues within 4Å: Chain C: N.1098, T.1100, H.1101, F.1103 No protein-ligand interaction detected (PLIP)

3 x NAG- NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-NAG.2: 4 residues within 4Å: Chain A: N.122, A.123, V.127, V.171 No protein-ligand interaction detected (PLIP) NAG-NAG-NAG.12: 4 residues within 4Å: Chain B: N.122, A.123, V.127, V.171 No protein-ligand interaction detected (PLIP) NAG-NAG-NAG.20: 4 residues within 4Å: Chain C: N.122, A.123, V.127, V.171 No protein-ligand interaction detected (PLIP)

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

NAG.27: 2 residues within 4Å: Chain A: Y.28, N.61 Ligand excluded by PLIP NAG.28: 1 residues within 4Å: Chain A: N.603 Ligand excluded by PLIP NAG.29: 5 residues within 4Å: Chain A: N.616, Q.644, T.645, R.646 Ligands: NAG.30 Ligand excluded by PLIP NAG.30: 1 residues within 4Å: Ligands: NAG.29 Ligand excluded by PLIP NAG.31: 1 residues within 4Å: Chain A: N.657 Ligand excluded by PLIP NAG.32: 3 residues within 4Å: Chain A: N.709, I.1130, G.1131 Ligand excluded by PLIP NAG.33: 4 residues within 4Å: Chain A: N.801, S.803, Q.804 Ligands: NAG.34 Ligand excluded by PLIP NAG.34: 1 residues within 4Å: Ligands: NAG.33 Ligand excluded by PLIP NAG.35: 2 residues within 4Å: Chain A: N.1134 Ligands: NAG.36 Ligand excluded by PLIP NAG.36: 1 residues within 4Å: Ligands: NAG.35 Ligand excluded by PLIP NAG.38: 2 residues within 4Å: Chain B: Y.28, N.61 Ligand excluded by PLIP NAG.39: 3 residues within 4Å: Chain B: G.339, N.343 Ligands: NAG.40 Ligand excluded by PLIP NAG.40: 2 residues within 4Å: Chain B: N.370 Ligands: NAG.39 Ligand excluded by PLIP NAG.41: 1 residues within 4Å: Chain B: N.603 Ligand excluded by PLIP NAG.42: 5 residues within 4Å: Chain B: N.616, Q.644, T.645, R.646 Ligands: NAG.43 Ligand excluded by PLIP NAG.43: 1 residues within 4Å: Ligands: NAG.42 Ligand excluded by PLIP NAG.44: 1 residues within 4Å: Chain B: N.657 Ligand excluded by PLIP NAG.45: 3 residues within 4Å: Chain B: N.709, I.1130, G.1131 Ligand excluded by PLIP NAG.46: 4 residues within 4Å: Chain B: N.801, S.803, Q.804 Ligands: NAG.47 Ligand excluded by PLIP NAG.47: 1 residues within 4Å: Ligands: NAG.46 Ligand excluded by PLIP NAG.48: 4 residues within 4Å: Chain B: A.706, E.1072, N.1074 Ligands: NAG.49 Ligand excluded by PLIP NAG.49: 2 residues within 4Å: Chain B: A.706 Ligands: NAG.48 Ligand excluded by PLIP NAG.50: 2 residues within 4Å: Chain B: N.1134 Ligands: NAG.51 Ligand excluded by PLIP NAG.51: 1 residues within 4Å: Ligands: NAG.50 Ligand excluded by PLIP NAG.53: 2 residues within 4Å: Chain C: Y.28, N.61 Ligand excluded by PLIP NAG.54: 3 residues within 4Å: Chain C: G.339, N.343 Ligands: NAG.55 Ligand excluded by PLIP NAG.55: 1 residues within 4Å: Ligands: NAG.54 Ligand excluded by PLIP NAG.56: 1 residues within 4Å: Chain C: N.603 Ligand excluded by PLIP NAG.57: 5 residues within 4Å: Chain C: N.616, Q.644, T.645, R.646 Ligands: NAG.58 Ligand excluded by PLIP NAG.58: 1 residues within 4Å: Ligands: NAG.57 Ligand excluded by PLIP NAG.59: 1 residues within 4Å: Chain C: N.657 Ligand excluded by PLIP NAG.60: 4 residues within 4Å: Chain A: D.796 Chain C: N.709, I.1130, G.1131 Ligand excluded by PLIP NAG.61: 4 residues within 4Å: Chain C: N.801, S.803, Q.804 Ligands: NAG.62 Ligand excluded by PLIP NAG.62: 1 residues within 4Å: Ligands: NAG.61 Ligand excluded by PLIP NAG.63: 4 residues within 4Å: Chain C: A.706, E.1072, N.1074 Ligands: NAG.64 Ligand excluded by PLIP NAG.64: 2 residues within 4Å: Chain C: A.706 Ligands: NAG.63 Ligand excluded by PLIP NAG.65: 2 residues within 4Å: Chain C: N.1134 Ligands: NAG.66 Ligand excluded by PLIP NAG.66: 1 residues within 4Å: Ligands: NAG.65 Ligand excluded by PLIP

3 x EIC: LINOLEIC ACID(Non-covalent)

EIC.37: 15 residues within 4Å: Chain A: C.336, P.337, F.338, I.358, A.363, Y.365, L.368, Y.369, F.377, L.387, V.395, I.434, L.513 Chain C: R.408, T.415 15 PLIP interactions: 13 interactions with chain A, 2 interactions with chain C Hydrophobic interactions: A:F.338, A:F.338, A:I.358, A:A.363, A:Y.365, A:Y.365, A:L.368, A:F.377, A:L.387, A:L.387, A:V.395, A:I.434, A:L.513 Hydrogen bonds: C:T.415 Salt bridges: C:R.408 EIC.52: 13 residues within 4Å: Chain A: R.408, Q.409, T.415, G.416 Chain B: F.338, I.358, A.363, Y.365, F.374, F.377, L.387, V.395, I.434 12 PLIP interactions: 11 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:F.338, B:I.358, B:A.363, B:Y.365, B:Y.365, B:F.374, B:F.377, B:L.387, B:L.387, B:V.395, B:I.434 Salt bridges: A:R.408 EIC.67: 13 residues within 4Å: Chain B: Q.409, G.416, K.417 Chain C: P.337, F.338, I.358, A.363, Y.365, Y.369, F.374, F.377, L.513, F.515 11 PLIP interactions: 3 interactions with chain B, 8 interactions with chain C Hydrogen bonds: B:Q.409, B:K.417 Salt bridges: B:R.408 Hydrophobic interactions: C:F.338, C:I.358, C:A.363, C:Y.365, C:Y.369, C:F.374, C:F.377, C:F.515

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhang, Z. et al., Defining the features and structure of neutralizing antibody targeting the silent face of the SARS-CoV-2 spike N-terminal domain. MedComm (2020) (2024)

Release Date

2024-06-05

Peptides

Spike glycoprotein: ABC
heavy chain of 3711: DFH
light chain of 3711: EGI

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
H

F
I

H
J

E
L

G
M

I
N

Spike glycoprotein

heavy chain of 3711

light chain of 3711

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