SMTL ID : 5w9h.1

MERS S ectodomain trimer in complex with variable domain of neutralizing antibody G4

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-6-3-3-mer

Ligands

21 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: 4 residues within 4Å: Chain A: N.1176 Chain B: Y.101, Y.102, D.104 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 4 residues within 4Å: Chain A: A.1158, P.1161, V.1209, N.1213 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 1 residues within 4Å: Chain A: N.785 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 2 residues within 4Å: Chain A: N.870, T.872 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 3 residues within 4Å: Chain D: N.785, Q.1003, S.1144 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 3 residues within 4Å: Chain D: V.1209, Y.1211, N.1213 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 3 residues within 4Å: Chain D: N.870, T.872, Q.1009 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 3 residues within 4Å: Chain D: N.1176 Chain E: Y.101, D.104 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 3 residues within 4Å: Chain G: N.785, Q.1003, N.1145 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 4 residues within 4Å: Chain G: N.1176 Chain H: Y.101, Y.102, D.104 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 3 residues within 4Å: Chain G: N.870, T.872, Q.1009 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 4 residues within 4Å: Chain G: A.1158, P.1161, V.1209, N.1213 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 2 residues within 4Å: Chain J: R.221, N.244 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 1 residues within 4Å: Chain J: N.66 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 5 residues within 4Å: Chain J: N.125, D.248, E.249, I.250, Y.274 2 PLIP interactions: 2 interactions with chain J Hydrogen bonds: J:D.248, J:Y.274 NAG-NAG.16: 1 residues within 4Å: Chain K: N.66 No protein-ligand interaction detected (PLIP) NAG-NAG.17: 7 residues within 4Å: Chain K: A.124, N.125, D.248, E.249, I.250, L.251, Y.274 1 PLIP interactions: 1 interactions with chain K Hydrogen bonds: K:Y.274 NAG-NAG.18: 5 residues within 4Å: Chain K: L.179, R.181, R.221, T.242, N.244 1 PLIP interactions: 1 interactions with chain K Hydrogen bonds: K:R.181 NAG-NAG.19: 5 residues within 4Å: Chain L: A.124, N.125, D.248, E.249, I.250 No protein-ligand interaction detected (PLIP) NAG-NAG.20: 2 residues within 4Å: Chain L: N.66, V.329 No protein-ligand interaction detected (PLIP) NAG-NAG.21: 3 residues within 4Å: Chain L: R.221, T.242, N.244 1 PLIP interactions: 1 interactions with chain L Hydrogen bonds: L:R.221

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

NAG.22: 1 residues within 4Å: Chain A: N.774 Ligand excluded by PLIP NAG.23: 1 residues within 4Å: Chain D: N.774 Ligand excluded by PLIP NAG.24: 2 residues within 4Å: Chain A: P.971 Chain G: N.774 Ligand excluded by PLIP NAG.25: 3 residues within 4Å: Chain J: Y.18, R.235, N.236 Ligand excluded by PLIP NAG.26: 5 residues within 4Å: Chain J: Q.37, F.40, D.41, N.104, Y.105 Ligand excluded by PLIP NAG.27: 2 residues within 4Å: Chain J: F.165, N.166 Ligand excluded by PLIP NAG.28: 5 residues within 4Å: Chain J: N.155, G.159, M.161 Chain L: S.546, P.547 Ligand excluded by PLIP NAG.29: 2 residues within 4Å: Chain J: N.719, S.721 Ligand excluded by PLIP NAG.30: 3 residues within 4Å: Chain J: N.619, C.620, N.647 Ligand excluded by PLIP NAG.31: 2 residues within 4Å: Chain K: F.165, N.166 Ligand excluded by PLIP NAG.32: 3 residues within 4Å: Chain K: Y.18, H.167, N.236 Ligand excluded by PLIP NAG.33: 3 residues within 4Å: Chain K: N.619, N.647, Y.649 Ligand excluded by PLIP NAG.34: 2 residues within 4Å: Chain K: N.719, S.721 Ligand excluded by PLIP NAG.35: 2 residues within 4Å: Chain K: Q.37, N.104 Ligand excluded by PLIP NAG.36: 3 residues within 4Å: Chain K: G.154, N.155, M.161 Ligand excluded by PLIP NAG.37: 4 residues within 4Å: Chain L: L.707, Q.708, N.719, S.721 Ligand excluded by PLIP NAG.38: 4 residues within 4Å: Chain L: Q.37, D.41, N.104, Q.107 Ligand excluded by PLIP NAG.39: 3 residues within 4Å: Chain K: S.528 Chain L: F.165, N.166 Ligand excluded by PLIP NAG.40: 4 residues within 4Å: Chain K: P.547, L.548 Chain L: N.155, G.159 Ligand excluded by PLIP NAG.41: 3 residues within 4Å: Chain L: N.619, D.645, N.647 Ligand excluded by PLIP NAG.42: 2 residues within 4Å: Chain L: Y.18, N.236 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pallesen, J. et al., Immunogenicity and structures of a rationally designed prefusion MERS-CoV spike antigen. Proc. Natl. Acad. Sci. U.S.A. (2017)

Release Date

2017-08-16

Peptides

MERS S: ADGJKL
G4 VH: BEH
G4 VL: CFI

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

D
D

G
G

J
p

K
q

L
r

B
B

E
E

H
H

C
C

F
F

I
I

MERS S

G4 VH

G4 VL

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