SMTL ID : 6j11.1 (2 other biounits)

MERS-CoV spike N-terminal domain and 7D10 scFv complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.00 Å

Oligo State

hetero-1-1-1-mer

Ligands

1 x NAG- NAG- BMA- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-MAN-MAN-MAN.1: 17 residues within 4Å: Chain A: V.2, D.3, G.5, P.6, R.164, N.205, F.222, M.223, Y.224 Chain B: E.13, P.40, T.42, S.43, Y.44, Y.64, R.110, Y.121 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:D.3, A:D.3, A:M.223, A:D.3, A:D.3, A:D.3, B:S.43, B:Y.44 Hydrophobic interactions: A:M.223

1 x NAG- NAG- BMA- MAN: alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN.2: 3 residues within 4Å: Chain A: I.18, N.87, Q.90 No protein-ligand interaction detected (PLIP)

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

NAG-NAG.3: 7 residues within 4Å: Chain A: Y.1, I.169, N.219 Chain C: S.32, G.33, Y.34, F.56 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:F.56 NAG-NAG.4: 2 residues within 4Å: Chain A: R.204, N.227 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- BMA: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA.5: 7 residues within 4Å: Chain A: G.104, A.105, A.107, N.108, E.232, I.233, Y.257 No protein-ligand interaction detected (PLIP)

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

NAG.6: 2 residues within 4Å: Chain A: N.49, V.312 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:V.312 Hydrogen bonds: A:N.49 NAG.7: 4 residues within 4Å: Chain A: N.138, F.139, S.140, G.142 No protein-ligand interaction detected (PLIP) NAG.8: 2 residues within 4Å: Chain A: S.135, N.149 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.135

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhou, H. et al., Structural definition of a neutralization epitope on the N-terminal domain of MERS-CoV spike glycoprotein. Nat Commun (2019)

Release Date

2019-07-24

Peptides

N-terminal domain of Spike glycoprotein: A
VH of 7D10: B
VL of 7D10: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
H

C
L

N-terminal domain of Spike glycoprotein

VH of 7D10

VL of 7D10

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