SMTL ID : 9mi3.1

Cryo-EM structure of SARS-CoV-2 spike protein in complex with neutralizing human antibody WRAIR-2008

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-3-mer

Ligands

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

NAG.1: 5 residues within 4Å: Chain A: N.1085, G.1086, T.1087, H.1088, F.1090 Ligand excluded by PLIP NAG.2: 3 residues within 4Å: Chain A: I.1119, V.1120, N.1121 Ligand excluded by PLIP NAG.3: 1 residues within 4Å: Chain A: N.644 Ligand excluded by PLIP NAG.4: 2 residues within 4Å: Chain A: N.603, T.605 Ligand excluded by PLIP NAG.5: 2 residues within 4Å: Chain A: Y.15, N.48 Ligand excluded by PLIP NAG.6: 3 residues within 4Å: Chain A: E.268, N.269 Chain H: K.545 Ligand excluded by PLIP NAG.7: 4 residues within 4Å: Chain A: P.317, N.318, P.566, Q.567 Ligand excluded by PLIP NAG.8: 4 residues within 4Å: Chain A: N.696, N.697, I.1117, G.1118 Ligand excluded by PLIP NAG.9: 4 residues within 4Å: Chain A: N.704, L.909, Q.913, Q.1058 Ligand excluded by PLIP NAG.10: 3 residues within 4Å: Chain A: N.788, S.790, Q.791 Ligand excluded by PLIP NAG.11: 6 residues within 4Å: Chain A: A.693, A.700, E.1059, K.1060, N.1061 Chain C: Q.882 Ligand excluded by PLIP NAG.12: 5 residues within 4Å: Chain C: N.1085, G.1086, T.1087, H.1088, F.1090 Ligand excluded by PLIP NAG.13: 4 residues within 4Å: Chain C: C.1069, I.1119, V.1120, N.1121 Ligand excluded by PLIP NAG.14: 1 residues within 4Å: Chain C: N.644 Ligand excluded by PLIP NAG.15: 4 residues within 4Å: Chain C: V.602, N.603, C.604, Q.631 Ligand excluded by PLIP NAG.16: 3 residues within 4Å: Chain C: N.267, E.268, N.269 Ligand excluded by PLIP NAG.17: 5 residues within 4Å: Chain C: F.316, P.317, N.318, I.319, Q.567 Ligand excluded by PLIP NAG.18: 3 residues within 4Å: Chain C: N.696, I.1117, G.1118 Ligand excluded by PLIP NAG.19: 3 residues within 4Å: Chain C: N.704, L.909, Q.913 Ligand excluded by PLIP NAG.20: 3 residues within 4Å: Chain C: N.788, S.790, Q.791 Ligand excluded by PLIP NAG.21: 4 residues within 4Å: Chain C: A.693, S.698, N.1061 Chain H: Q.882 Ligand excluded by PLIP NAG.22: 5 residues within 4Å: Chain A: Q.882 Chain H: A.693, S.695, S.698, N.1061 Ligand excluded by PLIP NAG.23: 1 residues within 4Å: Chain H: N.644 Ligand excluded by PLIP NAG.24: 4 residues within 4Å: Chain H: Y.15, S.47, N.48, V.49 Ligand excluded by PLIP NAG.25: 3 residues within 4Å: Chain H: N.696, I.1117, G.1118 Ligand excluded by PLIP NAG.26: 7 residues within 4Å: Chain H: N.704, F.705, T.706, L.909, Q.913, A.1057, Q.1058 Ligand excluded by PLIP NAG.27: 3 residues within 4Å: Chain H: N.788, S.790, Q.791 Ligand excluded by PLIP NAG.28: 4 residues within 4Å: Chain H: N.1085, T.1087, H.1088, F.1090 Ligand excluded by PLIP NAG.29: 3 residues within 4Å: Chain H: I.1119, V.1120, N.1121 Ligand excluded by PLIP NAG.30: 3 residues within 4Å: Chain H: N.603, T.605, Q.631 Ligand excluded by PLIP NAG.31: 4 residues within 4Å: Chain C: K.545 Chain H: N.267, E.268, N.269 Ligand excluded by PLIP NAG.32: 2 residues within 4Å: Chain H: N.318, Q.567 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Jensen, J.L. et al., Cryo-EM structure of SARS-CoV-2 spike protein in complex with neutralizing human antibody WRAIR-2008. To Be Published

Release Date

2025-08-20

Peptides

Spike glycoprotein: ACH
WRAIR-2008 antibody Fab heavy chain: BEG
WRAIR-2008 antibody Fab light chain: DFI

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

H
K

B
B

E
E

G
H

D
D

F
F

I
L

Spike glycoprotein

WRAIR-2008 antibody Fab heavy chain

WRAIR-2008 antibody Fab light chain

Related Entries With Identical Sequence