SMTL ID : 8g70.1

SARS-CoV-2 spike/nanobody mixture complex

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-3-1-2-mer

Ligands

12 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: 3 residues within 4Å: Chain A: N.704, L.909, Q.1058 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.909 NAG-NAG.2: 3 residues within 4Å: Chain A: N.788, S.790, Q.791 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 4 residues within 4Å: Chain A: N.1085, T.1087, H.1088, F.1090 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 1 residues within 4Å: Chain A: N.1121 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 3 residues within 4Å: Chain B: N.788, S.790, Q.791 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 4 residues within 4Å: Chain B: N.1085, T.1087, H.1088, F.1090 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 1 residues within 4Å: Chain B: N.1121 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 2 residues within 4Å: Chain C: N.704, L.909 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 3 residues within 4Å: Chain C: N.788, S.790, Q.791 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 4 residues within 4Å: Chain C: N.1085, T.1087, H.1088, F.1090 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 2 residues within 4Å: Chain C: I.1119, N.1121 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 5 residues within 4Å: Chain A: N.109, A.110, T.111, N.112, V.114 No protein-ligand interaction detected (PLIP)

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

NAG.13: 2 residues within 4Å: Chain A: N.318, K.516 Ligand excluded by PLIP NAG.14: 3 residues within 4Å: Chain A: G.326, N.330, L.355 Ligand excluded by PLIP NAG.15: 1 residues within 4Å: Chain A: N.603 Ligand excluded by PLIP NAG.16: 3 residues within 4Å: Chain A: H.642, V.643, N.644 Ligand excluded by PLIP NAG.17: 3 residues within 4Å: Chain A: N.696, G.1118 Chain B: D.783 Ligand excluded by PLIP NAG.18: 1 residues within 4Å: Chain A: N.1061 Ligand excluded by PLIP NAG.19: 2 residues within 4Å: Chain A: N.4, N.124 Ligand excluded by PLIP NAG.20: 6 residues within 4Å: Chain A: Y.15, N.48 Chain D: N.75, A.76, K.77, N.78 Ligand excluded by PLIP NAG.21: 1 residues within 4Å: Chain A: N.61 Ligand excluded by PLIP NAG.22: 1 residues within 4Å: Chain A: N.152 Ligand excluded by PLIP NAG.23: 1 residues within 4Å: Chain A: N.590 Ligand excluded by PLIP NAG.24: 5 residues within 4Å: Chain A: N.135, N.136, K.137, W.139, E.141 Ligand excluded by PLIP NAG.25: 1 residues within 4Å: Chain A: N.269 Ligand excluded by PLIP NAG.26: 4 residues within 4Å: Chain A: T.95, T.101, N.221, T.223 Ligand excluded by PLIP NAG.27: 2 residues within 4Å: Chain B: N.221, T.223 Ligand excluded by PLIP NAG.28: 2 residues within 4Å: Chain B: N.590, T.591 Ligand excluded by PLIP NAG.29: 3 residues within 4Å: Chain B: N.603, T.605, Q.631 Ligand excluded by PLIP NAG.30: 1 residues within 4Å: Chain B: N.644 Ligand excluded by PLIP NAG.31: 3 residues within 4Å: Chain B: N.696, G.1118 Chain C: D.783 Ligand excluded by PLIP NAG.32: 2 residues within 4Å: Chain B: N.704, Q.913 Ligand excluded by PLIP NAG.33: 2 residues within 4Å: Chain B: N.1061, T.1063 Ligand excluded by PLIP NAG.34: 3 residues within 4Å: Chain B: N.4, L.5, N.124 Ligand excluded by PLIP NAG.35: 2 residues within 4Å: Chain B: N.48 Chain E: A.76 Ligand excluded by PLIP NAG.36: 1 residues within 4Å: Chain B: N.61 Ligand excluded by PLIP NAG.37: 5 residues within 4Å: Chain B: N.151, N.152 Chain K: S.27, G.28, S.29 Ligand excluded by PLIP NAG.38: 2 residues within 4Å: Chain B: E.268, N.269 Ligand excluded by PLIP NAG.39: 4 residues within 4Å: Chain B: N.109, A.110, T.111, N.112 Ligand excluded by PLIP NAG.40: 2 residues within 4Å: Chain B: N.136, K.137 Ligand excluded by PLIP NAG.41: 1 residues within 4Å: Chain B: N.330 Ligand excluded by PLIP NAG.42: 2 residues within 4Å: Chain B: N.318, V.349 Ligand excluded by PLIP NAG.43: 6 residues within 4Å: Chain C: Y.15, N.48 Chain F: F.31, N.75, A.76, K.77 Ligand excluded by PLIP NAG.44: 4 residues within 4Å: Chain C: N.109, T.111, V.114, K.116 Ligand excluded by PLIP NAG.45: 3 residues within 4Å: Chain B: K.545 Chain C: E.268, N.269 Ligand excluded by PLIP NAG.46: 1 residues within 4Å: Chain C: N.318 Ligand excluded by PLIP NAG.47: 2 residues within 4Å: Chain C: N.603, T.605 Ligand excluded by PLIP NAG.48: 3 residues within 4Å: Chain C: H.642, V.643, N.644 Ligand excluded by PLIP NAG.49: 2 residues within 4Å: Chain C: N.696, G.1118 Ligand excluded by PLIP NAG.50: 2 residues within 4Å: Chain C: N.1061, T.1063 Ligand excluded by PLIP NAG.51: 5 residues within 4Å: Chain C: N.4, L.5, T.7, N.124, D.125 Ligand excluded by PLIP NAG.52: 3 residues within 4Å: Chain C: G.59, T.60, N.61 Ligand excluded by PLIP NAG.53: 2 residues within 4Å: Chain B: K.449 Chain C: N.152 Ligand excluded by PLIP NAG.54: 3 residues within 4Å: Chain C: F.329, N.330, S.360 Ligand excluded by PLIP NAG.55: 2 residues within 4Å: Chain C: N.590, T.591 Ligand excluded by PLIP NAG.56: 4 residues within 4Å: Chain C: H.133, N.135, N.136, W.139 Ligand excluded by PLIP NAG.57: 1 residues within 4Å: Chain C: N.221 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ye, G. et al., SARS-CoV-2 spike/nanobody mixture complex. To Be Published

Release Date

2024-02-21

Peptides

Spike glycoprotein: ABC
Nanosota-5: DEF
Nanosota-6: GHI
Nanosota-4: J
Nanosota-3: KL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
D

D
E

E
H

F
I

G
G

H
F

I
K

J
N

K
O

L
M

Spike glycoprotein

Nanosota-5

Nanosota-6

Nanosota-4

Nanosota-3

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