SMTL ID : 5w9i.1

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

Coordinates

PDB Format Compare

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: 3 residues within 4Å: Chain A: N.785, Q.1003, N.1145 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 2 residues within 4Å: Chain A: N.870, T.872 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 3 residues within 4Å: Chain A: V.1209, Y.1211, N.1213 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 4 residues within 4Å: Chain A: I.1147, N.1176 Chain C: Y.101, D.104 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 1 residues within 4Å: Chain B: N.66 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 2 residues within 4Å: Chain B: R.221, N.244 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 5 residues within 4Å: Chain B: N.125, D.248, E.249, I.250, Y.274 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 4 residues within 4Å: Chain E: N.785, S.787, Q.1003, N.1145 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 4 residues within 4Å: Chain E: I.1147, N.1176 Chain G: Y.101, D.104 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 4 residues within 4Å: Chain E: N.870, T.872, N.1002, G.1006 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 4 residues within 4Å: Chain E: S.776, V.1209, Y.1211, N.1213 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 2 residues within 4Å: Chain F: N.66, V.329 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 2 residues within 4Å: Chain F: R.221, N.244 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 3 residues within 4Å: Chain F: A.124, N.125, D.248 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 4 residues within 4Å: Chain I: S.776, V.1209, Y.1211, N.1213 No protein-ligand interaction detected (PLIP) NAG-NAG.16: 2 residues within 4Å: Chain I: N.870, T.872 No protein-ligand interaction detected (PLIP) NAG-NAG.17: 3 residues within 4Å: Chain I: N.785, S.787, Q.1003 No protein-ligand interaction detected (PLIP) NAG-NAG.18: 4 residues within 4Å: Chain I: I.1147, N.1176 Chain K: Y.101, D.104 No protein-ligand interaction detected (PLIP) NAG-NAG.19: 2 residues within 4Å: Chain J: R.221, N.244 No protein-ligand interaction detected (PLIP) NAG-NAG.20: 1 residues within 4Å: Chain J: N.66 No protein-ligand interaction detected (PLIP) NAG-NAG.21: 4 residues within 4Å: Chain J: A.124, N.125, I.250, Y.274 No protein-ligand interaction detected (PLIP)

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: 2 residues within 4Å: Chain B: Y.18, N.236 Ligand excluded by PLIP NAG.24: 3 residues within 4Å: Chain B: V.153, G.154, N.155 Ligand excluded by PLIP NAG.25: 2 residues within 4Å: Chain B: F.165, N.166 Ligand excluded by PLIP NAG.26: 4 residues within 4Å: Chain B: L.707, Q.708, N.719, S.721 Ligand excluded by PLIP NAG.27: 2 residues within 4Å: Chain B: N.619, C.620 Ligand excluded by PLIP NAG.28: 2 residues within 4Å: Chain B: N.104, Q.107 Ligand excluded by PLIP NAG.29: 1 residues within 4Å: Chain E: N.774 Ligand excluded by PLIP NAG.30: 4 residues within 4Å: Chain F: Y.18, I.186, R.235, N.236 Ligand excluded by PLIP NAG.31: 4 residues within 4Å: Chain F: L.707, Q.708, N.719, S.721 Ligand excluded by PLIP NAG.32: 2 residues within 4Å: Chain F: F.165, N.166 Ligand excluded by PLIP NAG.33: 3 residues within 4Å: Chain F: N.155, G.159, M.161 Ligand excluded by PLIP NAG.34: 2 residues within 4Å: Chain F: N.619, C.620 Ligand excluded by PLIP NAG.35: 2 residues within 4Å: Chain F: N.104, Q.107 Ligand excluded by PLIP NAG.36: 1 residues within 4Å: Chain I: N.774 Ligand excluded by PLIP NAG.37: 2 residues within 4Å: Chain J: N.104, Q.107 Ligand excluded by PLIP NAG.38: 2 residues within 4Å: Chain J: N.155, M.161 Ligand excluded by PLIP NAG.39: 3 residues within 4Å: Chain J: Q.708, N.719, S.721 Ligand excluded by PLIP NAG.40: 3 residues within 4Å: Chain J: Y.18, I.186, N.236 Ligand excluded by PLIP NAG.41: 2 residues within 4Å: Chain J: N.619, N.647 Ligand excluded by PLIP NAG.42: 3 residues within 4Å: Chain J: S.152, F.165, N.166 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

Spike glycoprotein: ABEFIJ
G4 VH: CGK
G4 VL: DHL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

E
E

F
F

I
I

J
J

C
C

G
G

K
K

D
D

H
H

L
L

Spike glycoprotein

G4 VH

G4 VL

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