SMTL ID : 5vyh.1

Crystal Structure of MERS-CoV S1 N-terminal Domain

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

monomer

Ligands

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

NAG.1: 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.2: 3 residues within 4Å: Chain A: I.18, N.87, Q.90 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:I.18 Water bridges: A:Q.90, A:Q.90 NAG.3: 6 residues within 4Å: Chain A: G.104, A.105, A.107, N.108, E.232, I.233 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.108, A:E.232 Water bridges: A:L.234 NAG.4: 3 residues within 4Å: Chain A: N.138, G.142, M.144 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.138 NAG.5: 2 residues within 4Å: Chain A: F.148, N.149 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.148 Water bridges: A:N.149 NAG.6: 8 residues within 4Å: Chain A: V.4, G.5, R.164, N.205, L.208, N.209, K.212, M.223 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.164, A:R.164, A:N.205, A:K.212 NAG.7: 3 residues within 4Å: Chain A: Y.1, I.169, N.219 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.219 NAG.8: 2 residues within 4Å: Chain A: R.204, N.227 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.204, A:R.204, A:N.227

1 x FOL: FOLIC ACID(Non-covalent)

FOL.9: 12 residues within 4Å: Chain A: W.27, P.28, R.29, P.30, H.64, A.106, G.111, T.112, I.123, W.293, A.294, A.295 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:W.27, A:P.28 Hydrogen bonds: A:P.28, A:T.112, A:T.112, A:T.112, A:W.293, A:A.295 Water bridges: A:R.29, A:R.29 Salt bridges: A:H.64 pi-Stacking: A:W.27, A:W.27, A:W.27

1 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.10: 9 residues within 4Å: Chain A: Y.127, N.227, I.228, E.235, F.237, S.250, R.252, Y.253, F.264 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:Y.127, A:I.228, A:F.237 Hydrogen bonds: A:E.235, A:S.250

1 x IMD: IMIDAZOLE(Non-covalent)

IMD.11: 5 residues within 4Å: Chain A: Y.60, L.304, D.321, G.323, F.324 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.321 pi-Stacking: A:Y.60

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

2017-08-30

Peptides

S protein: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

S protein