SMTL ID : 7wo4.1

SARS-CoV-2 Spike in complex with IgG 553-15 (S-553-15 dimer trimer )

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-6-6-6-mer

Ligands

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

NAG.1: 4 residues within 4Å: Chain A: K.113, E.132, N.164, N.165 Ligand excluded by PLIP NAG.2: 2 residues within 4Å: Chain A: N.331, Q.580 Ligand excluded by PLIP NAG.3: 4 residues within 4Å: Chain A: F.338, G.339, F.342, N.343 Ligand excluded by PLIP NAG.4: 3 residues within 4Å: Chain A: N.616, T.618, Q.644 Ligand excluded by PLIP NAG.5: 3 residues within 4Å: Chain A: N.709, I.1130, G.1131 Ligand excluded by PLIP NAG.6: 1 residues within 4Å: Chain A: N.717 Ligand excluded by PLIP NAG.7: 2 residues within 4Å: Chain A: A.706, N.1074 Ligand excluded by PLIP NAG.8: 1 residues within 4Å: Chain A: N.1134 Ligand excluded by PLIP NAG.9: 2 residues within 4Å: Chain A: E.281, N.282 Ligand excluded by PLIP NAG.10: 2 residues within 4Å: Chain A: Y.28, N.61 Ligand excluded by PLIP NAG.11: 2 residues within 4Å: Chain A: N.801, S.803 Ligand excluded by PLIP NAG.12: 4 residues within 4Å: Chain A: N.1098, T.1100, H.1101, F.1103 Ligand excluded by PLIP NAG.13: 3 residues within 4Å: Chain A: C.15, N.17, N.137 Ligand excluded by PLIP NAG.14: 5 residues within 4Å: Chain A: N.122, T.124, N.125, V.127, E.154 Ligand excluded by PLIP NAG.15: 4 residues within 4Å: Chain A: Y.145, N.148, N.149, M.153 Ligand excluded by PLIP NAG.16: 1 residues within 4Å: Chain B: N.1134 Ligand excluded by PLIP NAG.17: 4 residues within 4Å: Chain B: N.1098, T.1100, H.1101, F.1103 Ligand excluded by PLIP NAG.18: 3 residues within 4Å: Chain B: N.801, S.803, Q.804 Ligand excluded by PLIP NAG.19: 3 residues within 4Å: Chain B: N.717, L.922, Q.926 Ligand excluded by PLIP NAG.20: 3 residues within 4Å: Chain B: N.709, I.1130, G.1131 Ligand excluded by PLIP NAG.21: 2 residues within 4Å: Chain B: N.616, Q.644 Ligand excluded by PLIP NAG.22: 5 residues within 4Å: Chain B: F.338, G.339, F.342, N.343, V.367 Ligand excluded by PLIP NAG.23: 2 residues within 4Å: Chain B: N.331, Q.580 Ligand excluded by PLIP NAG.24: 2 residues within 4Å: Chain B: E.281, N.282 Ligand excluded by PLIP NAG.25: 3 residues within 4Å: Chain B: E.132, N.164, N.165 Ligand excluded by PLIP NAG.26: 3 residues within 4Å: Chain B: Y.28, T.29, N.61 Ligand excluded by PLIP NAG.27: 3 residues within 4Å: Chain B: C.15, N.17, N.137 Ligand excluded by PLIP NAG.28: 2 residues within 4Å: Chain B: N.149, S.151 Ligand excluded by PLIP NAG.29: 3 residues within 4Å: Chain B: N.122, A.123, N.125 Ligand excluded by PLIP NAG.30: 3 residues within 4Å: Chain B: A.706, N.1074 Chain C: Q.895 Ligand excluded by PLIP NAG.31: 3 residues within 4Å: Chain C: N.280, E.281, N.282 Ligand excluded by PLIP NAG.32: 3 residues within 4Å: Chain C: N.331, Q.580, T.581 Ligand excluded by PLIP NAG.33: 2 residues within 4Å: Chain C: N.343, V.367 Ligand excluded by PLIP NAG.34: 3 residues within 4Å: Chain C: N.616, T.618, Q.644 Ligand excluded by PLIP NAG.35: 2 residues within 4Å: Chain C: N.709, G.1131 Ligand excluded by PLIP NAG.36: 2 residues within 4Å: Chain C: N.717, L.922 Ligand excluded by PLIP NAG.37: 4 residues within 4Å: Chain C: A.706, E.1072, K.1073, N.1074 Ligand excluded by PLIP NAG.38: 1 residues within 4Å: Chain C: N.1134 Ligand excluded by PLIP NAG.39: 3 residues within 4Å: Chain C: N.801, S.803, Q.804 Ligand excluded by PLIP NAG.40: 3 residues within 4Å: Chain C: N.1098, H.1101, F.1103 Ligand excluded by PLIP NAG.41: 3 residues within 4Å: Chain C: C.15, N.17, N.137 Ligand excluded by PLIP NAG.42: 4 residues within 4Å: Chain C: H.146, N.148, N.149, M.153 Ligand excluded by PLIP NAG.43: 2 residues within 4Å: Chain C: Y.28, N.61 Ligand excluded by PLIP NAG.44: 5 residues within 4Å: Chain C: N.122, A.123, T.124, V.127, E.154 Ligand excluded by PLIP NAG.45: 3 residues within 4Å: Chain C: Q.115, E.132, N.165 Ligand excluded by PLIP NAG.46: 4 residues within 4Å: Chain J: K.113, E.132, N.164, N.165 Ligand excluded by PLIP NAG.47: 2 residues within 4Å: Chain J: N.331, Q.580 Ligand excluded by PLIP NAG.48: 3 residues within 4Å: Chain J: N.616, T.618, Q.644 Ligand excluded by PLIP NAG.49: 3 residues within 4Å: Chain J: N.709, I.1130, G.1131 Ligand excluded by PLIP NAG.50: 1 residues within 4Å: Chain J: N.717 Ligand excluded by PLIP NAG.51: 2 residues within 4Å: Chain J: A.706, N.1074 Ligand excluded by PLIP NAG.52: 1 residues within 4Å: Chain J: N.1134 Ligand excluded by PLIP NAG.53: 2 residues within 4Å: Chain J: E.281, N.282 Ligand excluded by PLIP NAG.54: 2 residues within 4Å: Chain J: Y.28, N.61 Ligand excluded by PLIP NAG.55: 2 residues within 4Å: Chain J: N.801, S.803 Ligand excluded by PLIP NAG.56: 4 residues within 4Å: Chain J: N.1098, T.1100, H.1101, F.1103 Ligand excluded by PLIP NAG.57: 4 residues within 4Å: Chain J: C.15, V.16, N.17, N.137 Ligand excluded by PLIP NAG.58: 4 residues within 4Å: Chain J: N.122, T.124, V.127, E.154 Ligand excluded by PLIP NAG.59: 4 residues within 4Å: Chain J: Y.145, N.148, N.149, M.153 Ligand excluded by PLIP NAG.60: 4 residues within 4Å: Chain J: G.339, F.342, N.343, V.367 Ligand excluded by PLIP NAG.61: 1 residues within 4Å: Chain K: N.1134 Ligand excluded by PLIP NAG.62: 4 residues within 4Å: Chain K: N.1098, T.1100, H.1101, F.1103 Ligand excluded by PLIP NAG.63: 3 residues within 4Å: Chain K: N.801, S.803, Q.804 Ligand excluded by PLIP NAG.64: 3 residues within 4Å: Chain K: N.717, L.922, Q.926 Ligand excluded by PLIP NAG.65: 3 residues within 4Å: Chain K: N.709, I.1130, G.1131 Ligand excluded by PLIP NAG.66: 2 residues within 4Å: Chain K: N.616, Q.644 Ligand excluded by PLIP NAG.67: 4 residues within 4Å: Chain K: F.338, G.339, F.342, N.343 Ligand excluded by PLIP NAG.68: 2 residues within 4Å: Chain K: N.331, Q.580 Ligand excluded by PLIP NAG.69: 2 residues within 4Å: Chain K: E.281, N.282 Ligand excluded by PLIP NAG.70: 3 residues within 4Å: Chain K: E.132, N.164, N.165 Ligand excluded by PLIP NAG.71: 3 residues within 4Å: Chain K: Y.28, T.29, N.61 Ligand excluded by PLIP NAG.72: 3 residues within 4Å: Chain K: C.15, N.17, N.137 Ligand excluded by PLIP NAG.73: 3 residues within 4Å: Chain K: N.149, K.150, S.151 Ligand excluded by PLIP NAG.74: 5 residues within 4Å: Chain K: N.122, A.123, T.124, N.125, V.127 Ligand excluded by PLIP NAG.75: 3 residues within 4Å: Chain K: A.706, N.1074 Chain L: Q.895 Ligand excluded by PLIP NAG.76: 3 residues within 4Å: Chain L: N.280, E.281, N.282 Ligand excluded by PLIP NAG.77: 3 residues within 4Å: Chain L: N.331, Q.580, T.581 Ligand excluded by PLIP NAG.78: 2 residues within 4Å: Chain L: G.339, N.343 Ligand excluded by PLIP NAG.79: 3 residues within 4Å: Chain L: N.616, T.618, Q.644 Ligand excluded by PLIP NAG.80: 2 residues within 4Å: Chain L: N.709, G.1131 Ligand excluded by PLIP NAG.81: 2 residues within 4Å: Chain L: N.717, L.922 Ligand excluded by PLIP NAG.82: 4 residues within 4Å: Chain L: A.706, E.1072, K.1073, N.1074 Ligand excluded by PLIP NAG.83: 1 residues within 4Å: Chain L: N.1134 Ligand excluded by PLIP NAG.84: 3 residues within 4Å: Chain L: N.801, S.803, Q.804 Ligand excluded by PLIP NAG.85: 3 residues within 4Å: Chain L: N.1098, H.1101, F.1103 Ligand excluded by PLIP NAG.86: 3 residues within 4Å: Chain L: C.15, N.17, N.137 Ligand excluded by PLIP NAG.87: 4 residues within 4Å: Chain L: H.146, N.148, N.149, M.153 Ligand excluded by PLIP NAG.88: 1 residues within 4Å: Chain L: N.61 Ligand excluded by PLIP NAG.89: 5 residues within 4Å: Chain L: N.122, A.123, T.124, V.127, E.154 Ligand excluded by PLIP NAG.90: 4 residues within 4Å: Chain L: Q.115, E.132, N.165, T.167 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhan, W. et al., Structural Study of SARS-CoV-2 Antibodies Identifies a Broad-Spectrum Antibody That Neutralizes the Omicron Variant by Disassembling the Spike Trimer. J.Virol. (2022)

Release Date

2022-07-20

Peptides

Spike glycoprotein: ABCJKL
mAb15 VH: DFHMOQ
mAb15 VL: EGINPR

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

J
J

K
K

L
L

D
D

F
F

H
H

M
M

O
O

Q
Q

E
E

G
G

I
I

N
N

P
P

R
R

Spike glycoprotein

mAb15 VH

mAb15 VL

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