SMTL ID : 6pz8.1

MERS S0 trimer in complex with variable domain of antibody G2

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-3-3-mer

Ligands

18 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: 2 residues within 4Å: Chain A: N.34, N.394 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 3 residues within 4Å: Chain A: I.396, E.397, N.425 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 5 residues within 4Å: Chain A: N.119, T.121, N.251, G.255, Q.258 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 6 residues within 4Å: Chain A: S.25, P.410, V.458, Y.460, Q.461, N.462 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 2 residues within 4Å: Chain B: F.148, N.149 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:F.148 NAG-NAG.8: 3 residues within 4Å: Chain B: I.169, R.218, N.219 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 2 residues within 4Å: Chain E: N.34, N.394 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 3 residues within 4Å: Chain E: I.396, E.397, N.425 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 5 residues within 4Å: Chain E: N.119, T.121, N.251, G.255, Q.258 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 6 residues within 4Å: Chain E: S.25, P.410, V.458, Y.460, Q.461, N.462 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 2 residues within 4Å: Chain F: F.148, N.149 1 PLIP interactions: 1 interactions with chain F Hydrophobic interactions: F:F.148 NAG-NAG.16: 3 residues within 4Å: Chain F: I.169, R.218, N.219 No protein-ligand interaction detected (PLIP) NAG-NAG.17: 2 residues within 4Å: Chain I: N.34, N.394 No protein-ligand interaction detected (PLIP) NAG-NAG.18: 3 residues within 4Å: Chain I: I.396, E.397, N.425 No protein-ligand interaction detected (PLIP) NAG-NAG.19: 5 residues within 4Å: Chain I: N.119, T.121, N.251, G.255, Q.258 No protein-ligand interaction detected (PLIP) NAG-NAG.20: 6 residues within 4Å: Chain I: S.25, P.410, V.458, Y.460, Q.461, N.462 No protein-ligand interaction detected (PLIP) NAG-NAG.22: 2 residues within 4Å: Chain J: F.148, N.149 1 PLIP interactions: 1 interactions with chain J Hydrophobic interactions: J:F.148 NAG-NAG.24: 3 residues within 4Å: Chain J: I.169, R.218, N.219 No protein-ligand interaction detected (PLIP)

3 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 B: G.104, A.107, N.108, E.232, I.233, L.234, Y.257 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Y.257 NAG-NAG-BMA.13: 7 residues within 4Å: Chain F: G.104, A.107, N.108, E.232, I.233, L.234, Y.257 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:Y.257 NAG-NAG-BMA.21: 7 residues within 4Å: Chain J: G.104, A.107, N.108, E.232, I.233, L.234, Y.257 1 PLIP interactions: 1 interactions with chain J Hydrogen bonds: J:Y.257

3 x NAG- NAG- BMA- MAN- MAN: 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.7: 6 residues within 4Å: Chain B: D.3, V.4, R.164, N.205, L.208, M.223 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:M.223 Hydrogen bonds: B:D.3, B:D.3, B:D.3, B:D.3 NAG-NAG-BMA-MAN-MAN.15: 6 residues within 4Å: Chain F: D.3, V.4, R.164, N.205, L.208, M.223 2 PLIP interactions: 2 interactions with chain F Hydrophobic interactions: F:M.223 Hydrogen bonds: F:D.3, F:D.3, F:D.3, F:D.3 NAG-NAG-BMA-MAN-MAN.23: 6 residues within 4Å: Chain J: D.3, V.4, R.164, N.205, L.208, M.223 2 PLIP interactions: 2 interactions with chain J Hydrophobic interactions: J:M.223 Hydrogen bonds: J:D.3, J:D.3, J:D.3, J:D.3

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

NAG.25: 3 residues within 4Å: Chain A: Q.21, L.22, N.23 Ligand excluded by PLIP NAG.26: 3 residues within 4Å: Chain A: L.8 Chain B: Q.691, N.702 Ligand excluded by PLIP NAG.27: 4 residues within 4Å: Chain B: N.602, C.603, T.604, N.630 Ligand excluded by PLIP NAG.28: 4 residues within 4Å: Chain B: S.48, N.49, V.312 Chain J: V.606 Ligand excluded by PLIP NAG.29: 2 residues within 4Å: Chain B: G.137, N.138 Ligand excluded by PLIP NAG.30: 4 residues within 4Å: Chain B: R.204, T.225, Y.226, N.227 Ligand excluded by PLIP NAG.31: 3 residues within 4Å: Chain E: Q.21, L.22, N.23 Ligand excluded by PLIP NAG.32: 3 residues within 4Å: Chain E: L.8 Chain F: Q.691, N.702 Ligand excluded by PLIP NAG.33: 4 residues within 4Å: Chain F: N.602, C.603, T.604, N.630 Ligand excluded by PLIP NAG.34: 4 residues within 4Å: Chain B: V.606 Chain F: S.48, N.49, V.312 Ligand excluded by PLIP NAG.35: 2 residues within 4Å: Chain F: G.137, N.138 Ligand excluded by PLIP NAG.36: 4 residues within 4Å: Chain F: R.204, T.225, Y.226, N.227 Ligand excluded by PLIP NAG.37: 3 residues within 4Å: Chain I: Q.21, L.22, N.23 Ligand excluded by PLIP NAG.38: 3 residues within 4Å: Chain I: L.8 Chain J: Q.691, N.702 Ligand excluded by PLIP NAG.39: 4 residues within 4Å: Chain J: N.602, C.603, T.604, N.630 Ligand excluded by PLIP NAG.40: 4 residues within 4Å: Chain F: V.606 Chain J: S.48, N.49, V.312 Ligand excluded by PLIP NAG.41: 2 residues within 4Å: Chain J: G.137, N.138 Ligand excluded by PLIP NAG.42: 4 residues within 4Å: Chain J: R.204, T.225, Y.226, N.227 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, N. et al., Structural Definition of a Neutralization-Sensitive Epitope on the MERS-CoV S1-NTD. Cell Rep (2019)

Release Date

2019-10-09

Peptides

S protein: AEI
S protein: BFJ
G2 heavy chain: CGK
G2 light chain: DHL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

E
E

I
I

B
B

F
J

J
F

C
H

G
C

K
D

D
L

H
G

L
K

S protein

S protein

G2 heavy chain

G2 light chain

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