SMTL ID : 7x08.1

S protein of SARS-CoV-2 in complex with 2G1

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-3-mer

Ligands

24 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: 1 residues within 4Å: Chain A: N.331 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 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.3: 3 residues within 4Å: Chain A: A.706, E.1072, N.1074 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 4 residues within 4Å: Chain A: N.1098, T.1100, H.1101, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 1 residues within 4Å: Chain B: N.331 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 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.7: 4 residues within 4Å: Chain B: N.1098, T.1100, H.1101, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 1 residues within 4Å: Chain C: N.331 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 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.10: 4 residues within 4Å: Chain C: N.1098, T.1100, H.1101, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 3 residues within 4Å: Chain A: C.15, N.17, N.137 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 4 residues within 4Å: Chain A: N.616, Q.644, T.645, R.646 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 3 residues within 4Å: Chain A: N.801, S.803, Q.804 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 1 residues within 4Å: Chain A: N.1134 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 3 residues within 4Å: Chain B: C.15, N.17, N.137 No protein-ligand interaction detected (PLIP) NAG-NAG.16: 4 residues within 4Å: Chain B: N.616, Q.644, T.645, R.646 No protein-ligand interaction detected (PLIP) NAG-NAG.17: 3 residues within 4Å: Chain B: N.801, S.803, Q.804 No protein-ligand interaction detected (PLIP) NAG-NAG.18: 3 residues within 4Å: Chain B: A.706, E.1072, N.1074 No protein-ligand interaction detected (PLIP) NAG-NAG.19: 1 residues within 4Å: Chain B: N.1134 No protein-ligand interaction detected (PLIP) NAG-NAG.20: 3 residues within 4Å: Chain C: C.15, N.17, N.137 No protein-ligand interaction detected (PLIP) NAG-NAG.21: 4 residues within 4Å: Chain C: N.616, Q.644, T.645, R.646 No protein-ligand interaction detected (PLIP) NAG-NAG.22: 3 residues within 4Å: Chain C: N.801, S.803, Q.804 No protein-ligand interaction detected (PLIP) NAG-NAG.23: 3 residues within 4Å: Chain C: A.706, E.1072, N.1074 No protein-ligand interaction detected (PLIP) NAG-NAG.24: 1 residues within 4Å: Chain C: N.1134 No protein-ligand interaction detected (PLIP)

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

NAG.25: 1 residues within 4Å: Chain A: N.61 Ligand excluded by PLIP NAG.26: 5 residues within 4Å: Chain A: N.122, T.124, N.125, V.127, K.129 Ligand excluded by PLIP NAG.27: 4 residues within 4Å: Chain A: H.146, N.148, N.149, M.153 Ligand excluded by PLIP NAG.28: 2 residues within 4Å: Chain A: N.164, N.165 Ligand excluded by PLIP NAG.29: 4 residues within 4Å: Chain A: N.234 Chain C: S.459, N.460, K.462 Ligand excluded by PLIP NAG.30: 1 residues within 4Å: Chain A: N.282 Ligand excluded by PLIP NAG.31: 3 residues within 4Å: Chain A: N.343, S.371, A.372 Ligand excluded by PLIP NAG.32: 1 residues within 4Å: Chain A: N.603 Ligand excluded by PLIP NAG.33: 1 residues within 4Å: Chain A: N.657 Ligand excluded by PLIP NAG.34: 3 residues within 4Å: Chain A: N.709, I.1130, G.1131 Ligand excluded by PLIP NAG.37: 1 residues within 4Å: Chain B: N.61 Ligand excluded by PLIP NAG.38: 5 residues within 4Å: Chain B: N.122, T.124, N.125, V.127, K.129 Ligand excluded by PLIP NAG.39: 4 residues within 4Å: Chain B: H.146, N.148, N.149, M.153 Ligand excluded by PLIP NAG.40: 2 residues within 4Å: Chain B: N.164, N.165 Ligand excluded by PLIP NAG.41: 3 residues within 4Å: Chain A: S.459, K.462 Chain B: N.234 Ligand excluded by PLIP NAG.42: 1 residues within 4Å: Chain B: N.282 Ligand excluded by PLIP NAG.43: 1 residues within 4Å: Chain B: N.343 Ligand excluded by PLIP NAG.44: 1 residues within 4Å: Chain B: N.603 Ligand excluded by PLIP NAG.45: 1 residues within 4Å: Chain B: N.657 Ligand excluded by PLIP NAG.46: 3 residues within 4Å: Chain B: N.709, I.1130, G.1131 Ligand excluded by PLIP NAG.48: 1 residues within 4Å: Chain C: N.61 Ligand excluded by PLIP NAG.49: 5 residues within 4Å: Chain C: N.122, T.124, N.125, V.127, K.129 Ligand excluded by PLIP NAG.50: 4 residues within 4Å: Chain C: H.146, N.148, N.149, M.153 Ligand excluded by PLIP NAG.51: 2 residues within 4Å: Chain C: N.164, N.165 Ligand excluded by PLIP NAG.52: 4 residues within 4Å: Chain B: S.459, N.460, K.462 Chain C: N.234 Ligand excluded by PLIP NAG.53: 1 residues within 4Å: Chain C: N.282 Ligand excluded by PLIP NAG.54: 4 residues within 4Å: Chain C: F.342, N.343, L.441, R.509 Ligand excluded by PLIP NAG.55: 1 residues within 4Å: Chain C: N.603 Ligand excluded by PLIP NAG.56: 1 residues within 4Å: Chain C: N.657 Ligand excluded by PLIP NAG.57: 4 residues within 4Å: Chain A: D.796 Chain C: N.709, I.1130, G.1131 Ligand excluded by PLIP

3 x EIC: LINOLEIC ACID(Non-covalent)

EIC.35: 17 residues within 4Å: Chain A: C.336, P.337, F.338, F.342, Y.365, L.368, Y.369, F.374, F.377, L.387, F.392, V.395, L.513, F.515 Chain C: R.408, T.415, G.416 17 PLIP interactions: 2 interactions with chain C, 15 interactions with chain A Hydrogen bonds: C:T.415 Salt bridges: C:R.408 Hydrophobic interactions: A:F.338, A:F.338, A:F.342, A:Y.365, A:Y.365, A:Y.365, A:L.368, A:F.374, A:F.377, A:L.387, A:L.387, A:F.392, A:V.395, A:L.513, A:F.515 EIC.36: 12 residues within 4Å: Chain A: R.408, Q.409, T.415, G.416 Chain B: F.338, I.358, Y.365, Y.369, F.374, F.377, L.387, F.392 10 PLIP interactions: 7 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:F.338, B:I.358, B:Y.369, B:F.374, B:L.387, B:L.387, B:F.392 Hydrogen bonds: A:T.415, A:T.415 Salt bridges: A:R.408 EIC.47: 14 residues within 4Å: Chain B: R.408, Q.409, G.416, K.417 Chain C: P.337, F.338, A.363, Y.365, Y.369, F.374, F.377, L.387, F.392, L.513 13 PLIP interactions: 10 interactions with chain C, 3 interactions with chain B Hydrophobic interactions: C:F.338, C:A.363, C:Y.365, C:Y.365, C:Y.369, C:F.374, C:F.374, C:L.387, C:F.392, C:L.513 Hydrogen bonds: B:Q.409, B:K.417 Salt bridges: B:R.408

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ma, H. et al., Broad ultra-potent neutralization of SARS-CoV-2 variants by monoclonal antibodies specific to the tip of RBD. Cell Discov (2022)

Release Date

2022-03-09

Peptides

Spike glycoprotein: ABC
heavy chain of 2G1: DFH
light chain of 2G1: 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 2G1

light chain of 2G1

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