SMTL ID : 7y0n.1

SARS-CoV-2 WT Spike in complex with R15 Fab and P14 Nanobody

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-3-3-mer

Ligands

15 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 B: R.328, N.331, Q.580 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 3 residues within 4Å: Chain B: N.717, L.922, Q.926 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 2 residues within 4Å: Chain B: N.801, Q.804 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 1 residues within 4Å: Chain B: N.1134 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 4 residues within 4Å: Chain B: N.1098, T.1100, H.1101, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 3 residues within 4Å: Chain A: R.328, N.331, Q.580 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 3 residues within 4Å: Chain A: N.717, L.922, Q.926 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 2 residues within 4Å: Chain A: N.801, Q.804 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 1 residues within 4Å: Chain A: N.1134 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: 3 residues within 4Å: Chain D: R.328, N.331, Q.580 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 3 residues within 4Å: Chain D: N.717, L.922, Q.926 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 2 residues within 4Å: Chain D: N.801, Q.804 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 1 residues within 4Å: Chain D: N.1134 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 4 residues within 4Å: Chain D: N.1098, T.1100, H.1101, F.1103 No protein-ligand interaction detected (PLIP)

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

NAG.16: 3 residues within 4Å: Chain A: Y.28, F.59, N.61 Ligand excluded by PLIP NAG.17: 3 residues within 4Å: Chain A: N.122, N.125, V.127 Ligand excluded by PLIP NAG.18: 2 residues within 4Å: Chain A: N.164, N.165 Ligand excluded by PLIP NAG.19: 1 residues within 4Å: Chain A: N.234 Ligand excluded by PLIP NAG.20: 2 residues within 4Å: Chain A: E.281, N.282 Ligand excluded by PLIP NAG.21: 3 residues within 4Å: Chain A: G.339, F.342, N.343 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: 1 residues within 4Å: Chain A: N.657 Ligand excluded by PLIP NAG.25: 2 residues within 4Å: Chain A: N.709, G.1131 Ligand excluded by PLIP NAG.26: 1 residues within 4Å: Chain A: N.1074 Ligand excluded by PLIP NAG.27: 3 residues within 4Å: Chain B: Y.28, F.59, N.61 Ligand excluded by PLIP NAG.28: 4 residues within 4Å: Chain B: V.120, N.122, N.125, V.127 Ligand excluded by PLIP NAG.29: 2 residues within 4Å: Chain B: N.164, N.165 Ligand excluded by PLIP NAG.30: 1 residues within 4Å: Chain B: N.234 Ligand excluded by PLIP NAG.31: 2 residues within 4Å: Chain B: E.281, N.282 Ligand excluded by PLIP NAG.32: 3 residues within 4Å: Chain B: G.339, F.342, N.343 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, T.618 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 B: N.709, G.1131 Ligand excluded by PLIP NAG.37: 1 residues within 4Å: Chain B: N.1074 Ligand excluded by PLIP NAG.38: 3 residues within 4Å: Chain D: Y.28, F.59, N.61 Ligand excluded by PLIP NAG.39: 4 residues within 4Å: Chain D: V.120, N.122, N.125, V.127 Ligand excluded by PLIP NAG.40: 2 residues within 4Å: Chain D: N.164, N.165 Ligand excluded by PLIP NAG.41: 1 residues within 4Å: Chain D: N.234 Ligand excluded by PLIP NAG.42: 2 residues within 4Å: Chain D: E.281, N.282 Ligand excluded by PLIP NAG.43: 3 residues within 4Å: Chain D: G.339, F.342, N.343 Ligand excluded by PLIP NAG.44: 1 residues within 4Å: Chain D: N.603 Ligand excluded by PLIP NAG.45: 2 residues within 4Å: Chain D: N.616, T.618 Ligand excluded by PLIP NAG.46: 1 residues within 4Å: Chain D: N.657 Ligand excluded by PLIP NAG.47: 2 residues within 4Å: Chain D: N.709, G.1131 Ligand excluded by PLIP NAG.48: 1 residues within 4Å: Chain D: N.1074 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, L., SARS-CoV-2 WT Spike in complex with R15 Fab and P14 Nanobody. To Be Published

Release Date

2023-09-13

Peptides

Spike glycoprotein: ABD
Heavy chain of R15-F7: CEF
P14 Nanobody: GHI
Light chain of R15-F7: JKL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

D
D

C
C

E
E

F
F

G
G

H
H

I
I

J
J

K
K

L
L

Spike glycoprotein

Heavy chain of R15-F7

P14 Nanobody

Light chain of R15-F7

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