SMTL ID : 5ej0.1

The vaccinia virus H3 envelope protein, a major target of neutralizing antibodies, exhibits a glycosyltransferase fold and binds UDP-Glucose

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

monomer

Ligands

1 x DHL: 2-AMINO-ETHANETHIOL(Non-covalent)

DHL.1: 12 residues within 4Å: Chain A: F.79, S.80, G.81, F.82, C.83, M.86, C.87, K.92, L.205, S.206, F.209 Ligands: MOH.24 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.81

4 x PG0: 2-(2-METHOXYETHOXY)ETHANOL(Non-functional Binders)

PG0.2: 8 residues within 4Å: Chain A: S.206, S.207, G.208, F.209, Y.210, F.211 Ligands: PG0.4, POL.8 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.208, A:F.209, A:Y.210, A:F.211 PG0.3: 5 residues within 4Å: Chain A: P.9, R.13, Q.63, T.65, N.68 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.13, A:R.13, A:N.123 Water bridges: A:N.68 PG0.4: 5 residues within 4Å: Chain A: S.207, G.208, F.211 Ligands: PG0.2, POL.8 1 PLIP interactions: 1 interactions with chain A Water bridges: A:S.207 PG0.5: 7 residues within 4Å: Chain A: D.146, T.191, M.220, K.221, I.222 Ligands: GOL.6, MOH.20 No protein-ligand interaction detected (PLIP)

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 4 residues within 4Å: Chain A: R.188, T.190 Ligands: PG0.5, MOH.20 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.190 Water bridges: A:R.188, A:T.190 GOL.7: 9 residues within 4Å: Chain A: W.102, I.147, Q.149, V.180, S.181, L.182, Y.185, E.217, R.224 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.149, A:Y.185, A:E.217

1 x POL: N-PROPANOL(Non-covalent)

POL.8: 4 residues within 4Å: Chain A: S.207, G.208 Ligands: PG0.2, PG0.4 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.207

2 x PDO: 1,3-PROPANDIOL(Non-covalent)

PDO.9: 3 residues within 4Å: Chain A: N.218, E.219, K.221 1 PLIP interactions: 1 interactions with chain A Water bridges: A:E.219 PDO.10: 9 residues within 4Å: Chain A: N.94, E.122, R.151, L.182, S.183, Y.210, H.236 Ligands: MOH.22, MG.25 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:N.94, A:E.122, A:R.151, A:Y.210, A:H.236 Water bridges: A:L.182

5 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.11: 3 residues within 4Å: Chain A: I.154, G.177, Y.178 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.178 EDO.12: 3 residues within 4Å: Chain A: N.21, E.128, D.129 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.129 Water bridges: A:N.21, A:N.21, A:I.130 EDO.13: 3 residues within 4Å: Chain A: S.80, G.81, G.203 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.81, A:G.203 EDO.14: 6 residues within 4Å: Chain A: I.153, Y.178, D.179, V.180, Y.210, F.211 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.178, A:V.180 Water bridges: A:V.180 EDO.15: 2 residues within 4Å: Chain A: D.58, Y.59 No protein-ligand interaction detected (PLIP)

3 x EOH: ETHANOL(Non-functional Binders)

EOH.16: 5 residues within 4Å: Chain A: T.175, I.222, N.223, R.224 Ligands: EOH.18 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:T.175 Hydrogen bonds: A:R.224, A:R.224 EOH.17: 7 residues within 4Å: Chain A: K.30, T.65, G.66, G.67, N.68, N.71, Y.75 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.30, A:G.67, A:N.68 EOH.18: 6 residues within 4Å: Chain A: G.177, A.214, E.217, N.218, R.224 Ligands: EOH.16 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:E.217, A:R.224 Hydrogen bonds: A:A.214, A:N.218, A:R.224

6 x MOH: METHANOL(Non-functional Binders)

MOH.19: 2 residues within 4Å: Chain A: D.124, D.237 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.124 MOH.20: 5 residues within 4Å: Chain A: K.144, D.146, R.188 Ligands: PG0.5, GOL.6 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.144, A:R.188 MOH.21: 3 residues within 4Å: Chain A: A.231, E.235, H.236 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:A.231 MOH.22: 5 residues within 4Å: Chain A: N.94, E.122, D.124 Ligands: PDO.10, MG.25 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.124 MOH.23: 0 residues within 4Å: (No contacts) 1 PLIP interactions: 1 interactions with chain A Water bridges: A:K.160 MOH.24: 5 residues within 4Å: Chain A: T.76, F.79, S.80, K.92 Ligands: DHL.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.80

1 x MG: MAGNESIUM ION(Non-covalent)

MG.25: 7 residues within 4Å: Chain A: E.122, D.124, N.125, S.183, H.236 Ligands: PDO.10, MOH.22 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:E.122, A:D.124, A:S.183

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Singh, K. et al., The Vaccinia Virus H3 Envelope Protein, a Major Target of Neutralizing Antibodies, Exhibits a Glycosyltransferase Fold and Binds UDP-Glucose. J.Virol. (2016)

Release Date

2016-03-16

Peptides

Envelope protein H3: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Envelope protein H3