SMTL ID : 7z9r.1

CRYO-EM STRUCTURE OF SARS-COV-2 SPIKE : H11-H4 Q98R H100E nanobody complex in 2Up1Down conformation

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-mer

Ligands

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

NAG-NAG.1: 4 residues within 4Å: Chain A: N.122, T.124, N.125, V.171 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.125 NAG-NAG.2: 3 residues within 4Å: Chain A: T.108, N.234, T.236 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 3 residues within 4Å: Chain A: N.280, E.281, N.282 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 4 residues within 4Å: Chain A: N.331, P.579, Q.580, T.581 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 5 residues within 4Å: Chain A: N.717, F.718, L.922, Q.926, Q.1071 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:Q.926 NAG-NAG.6: 4 residues within 4Å: Chain A: N.801, S.803, Q.804, F.817 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.817 Hydrogen bonds: A:Q.804 NAG-NAG.7: 4 residues within 4Å: Chain A: N.1098, T.1100, H.1101, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 3 residues within 4Å: Chain A: I.1132, V.1133, N.1134 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 5 residues within 4Å: Chain B: T.716, N.717, L.922, Q.926, Q.1071 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 3 residues within 4Å: Chain B: N.801, S.803, Q.804 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:Q.804 Hydrogen bonds: B:S.803, B:Q.804 NAG-NAG.11: 4 residues within 4Å: Chain B: N.1098, T.1100, H.1101, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 1 residues within 4Å: Chain B: N.1134 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 6 residues within 4Å: Chain C: N.122, T.124, N.125, V.127, K.129, V.171 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 3 residues within 4Å: Chain C: N.280, E.281, N.282 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 3 residues within 4Å: Chain C: N.709, I.1130, G.1131 No protein-ligand interaction detected (PLIP) NAG-NAG.16: 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:Q.926 NAG-NAG.17: 3 residues within 4Å: Chain C: N.801, S.803, Q.804 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:Q.804 NAG-NAG.18: 8 residues within 4Å: Chain B: Q.895 Chain C: N.703, S.704, A.706, A.713, E.1072, K.1073, N.1074 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.703 NAG-NAG.19: 5 residues within 4Å: Chain C: N.1098, T.1100, H.1101, F.1103, I.1114 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:F.1103, C:I.1114 NAG-NAG.20: 3 residues within 4Å: Chain C: C.1126, D.1127, N.1134 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:D.1127

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

NAG.21: 4 residues within 4Å: Chain A: Y.28, F.59, S.60, N.61 Ligand excluded by PLIP NAG.22: 1 residues within 4Å: Chain A: N.603 Ligand excluded by PLIP NAG.23: 2 residues within 4Å: Chain A: N.616, T.618 Ligand excluded by PLIP NAG.24: 2 residues within 4Å: Chain A: H.655, N.657 Ligand excluded by PLIP NAG.25: 2 residues within 4Å: Chain A: N.709, G.1131 Ligand excluded by PLIP NAG.26: 4 residues within 4Å: Chain A: A.713, E.1072, K.1073, N.1074 Ligand excluded by PLIP NAG.27: 4 residues within 4Å: Chain A: K.113, E.132, N.164, N.165 Ligand excluded by PLIP NAG.28: 6 residues within 4Å: Chain A: F.338, G.339, F.342, N.343, V.367, L.368 Ligand excluded by PLIP NAG.29: 2 residues within 4Å: Chain B: Y.28, N.61 Ligand excluded by PLIP NAG.30: 6 residues within 4Å: Chain B: N.122, T.124, N.125, V.127, E.169, V.171 Ligand excluded by PLIP NAG.31: 3 residues within 4Å: Chain B: N.280, E.281, N.282 Ligand excluded by PLIP NAG.32: 2 residues within 4Å: Chain B: N.331, Q.580 Ligand excluded by PLIP NAG.33: 1 residues within 4Å: Chain B: N.603 Ligand excluded by PLIP NAG.34: 2 residues within 4Å: Chain B: N.616, Q.644 Ligand excluded by PLIP NAG.35: 1 residues within 4Å: Chain B: N.657 Ligand excluded by PLIP NAG.36: 2 residues within 4Å: Chain A: D.796 Chain B: N.709 Ligand excluded by PLIP NAG.37: 4 residues within 4Å: Chain B: A.706, E.1072, K.1073, N.1074 Ligand excluded by PLIP NAG.38: 5 residues within 4Å: Chain B: F.338, G.339, N.343, V.367, L.368 Ligand excluded by PLIP NAG.39: 5 residues within 4Å: Chain B: N.196, G.199, G.232, I.233, N.234 Ligand excluded by PLIP NAG.40: 2 residues within 4Å: Chain C: Y.28, N.61 Ligand excluded by PLIP NAG.41: 1 residues within 4Å: Chain C: N.234 Ligand excluded by PLIP NAG.42: 1 residues within 4Å: Chain C: N.603 Ligand excluded by PLIP NAG.43: 2 residues within 4Å: Chain C: N.616, T.618 Ligand excluded by PLIP NAG.44: 3 residues within 4Å: Chain C: H.655, V.656, N.657 Ligand excluded by PLIP NAG.45: 6 residues within 4Å: Chain C: K.113, T.114, Q.115, E.132, N.165, T.167 Ligand excluded by PLIP NAG.46: 4 residues within 4Å: Chain C: P.330, N.331, I.332, Q.580 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mikolajek, H. et al., Correlation between the binding affinity and the conformational entropy of nanobody SARS-CoV-2 spike protein complexes. Proc.Natl.Acad.Sci.USA (2022)

Release Date

2022-07-13

Peptides

Spike glycoprotein,Fibritin: ABC
Nanobody H11-H4 Q98R H100E: DEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
Y

E
X

F
Z

Spike glycoprotein,Fibritin

Nanobody H11-H4 Q98R H100E

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