SMTL ID : 4adi.1

Crystal structure of the Rubella virus envelope glycoprotein E1 in post-fusion form (crystal form I)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-trimer

Ligands

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

NAG.1: 3 residues within 4Å: Chain A: A.72, R.73, N.76 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:A.72 Hydrogen bonds: A:N.76 Water bridges: A:A.72, A:N.76 NAG.12: 3 residues within 4Å: Chain A: Q.168, S.175, N.177 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.168, A:S.175, A:S.175, A:N.177 NAG.15: 2 residues within 4Å: Chain B: A.72, N.76 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:A.72 Hydrogen bonds: B:N.76 NAG.25: 3 residues within 4Å: Chain B: Q.168, S.175, N.177 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Q.168, B:S.175, B:S.175, B:N.177 NAG.28: 3 residues within 4Å: Chain C: A.72, R.73, N.76 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:A.72 Hydrogen bonds: C:N.76 NAG.39: 4 residues within 4Å: Chain C: R.27, Q.168, S.175, N.177 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:R.27, C:Q.168, C:S.175, C:S.175, C:N.177

15 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 8 residues within 4Å: Chain A: L.43, E.44, A.45, I.291, A.293 Chain C: H.428, T.429, T.430 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.44, A:A.45, A:I.291, A:A.293 GOL.3: 7 residues within 4Å: Chain A: R.80, A.81, C.82, A.116, E.118, R.252 Chain B: L.264 7 PLIP interactions: 4 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:C.82, A:C.82, A:E.118, A:R.252 Water bridges: B:R.256, B:R.256, B:R.256 GOL.4: 9 residues within 4Å: Chain A: T.9, A.10, P.11, H.317, P.319 Chain C: F.380, V.386, T.387 Ligands: GOL.34 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:T.387, A:P.319 Water bridges: C:V.386, C:A.388 GOL.5: 5 residues within 4Å: Chain A: A.362, P.363, G.364, P.382, G.383 1 PLIP interactions: 1 interactions with chain A Water bridges: A:G.364 GOL.6: 8 residues within 4Å: Chain A: D.259, D.261, D.262, P.263 Chain C: K.110, Q.111, P.114 Ligands: PEG.11 4 PLIP interactions: 1 interactions with chain C, 3 interactions with chain A Hydrogen bonds: C:Q.111, A:D.262 Water bridges: A:H.125, A:D.262 GOL.7: 3 residues within 4Å: Chain A: S.100, Y.101, Y.108 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.100, A:S.100 Water bridges: A:Y.101, A:Y.101 GOL.16: 9 residues within 4Å: Chain B: T.347, G.348, P.355, A.356, L.357 Chain C: R.217, H.308, T.311, T.312 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain C Hydrogen bonds: B:T.347, B:T.347, C:R.217, C:T.311 GOL.17: 6 residues within 4Å: Chain B: A.99, S.100, F.102, N.103, P.121, F.123 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:F.102, B:F.102 GOL.18: 3 residues within 4Å: Chain B: S.100, Y.101, Y.108 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.100 GOL.29: 2 residues within 4Å: Chain C: R.342 Ligands: GOL.30 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:R.342 GOL.30: 5 residues within 4Å: Chain C: R.342, A.362, P.363, G.364 Ligands: GOL.29 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:R.342, C:R.342, C:G.383 Water bridges: C:G.364 GOL.31: 5 residues within 4Å: Chain B: K.110, Q.111, P.114 Chain C: D.261, D.262 4 PLIP interactions: 4 interactions with chain C Water bridges: C:G.124, C:D.259, C:D.261, C:D.262 GOL.32: 9 residues within 4Å: Chain A: R.217, H.308, T.311, T.312 Chain C: T.347, G.348, P.355, A.356, L.357 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:R.217, A:T.311, C:P.355 Water bridges: A:R.217 GOL.33: 3 residues within 4Å: Chain C: S.100, Y.101, Y.108 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:S.100 Water bridges: C:Y.101 GOL.34: 6 residues within 4Å: Chain A: S.313, D.314 Chain C: V.386, T.387, A.388 Ligands: GOL.4 8 PLIP interactions: 4 interactions with chain A, 4 interactions with chain C Hydrogen bonds: A:S.313, A:D.314, C:V.386, C:T.387, C:A.388 Water bridges: A:S.313, A:H.317, C:A.388

3 x NA: SODIUM ION(Non-functional Binders)

NA.8: 4 residues within 4Å: Chain A: N.88, A.89, D.136, T.137 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.136, A:D.136 NA.19: 4 residues within 4Å: Chain B: N.88, A.89, D.136, T.137 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.88, B:D.136 Water bridges: B:S.91 NA.35: 4 residues within 4Å: Chain C: N.88, A.89, D.136, T.137 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:N.88, C:D.136

7 x ACT: ACETATE ION(Non-functional Binders)

ACT.9: 5 residues within 4Å: Chain A: Y.90, S.91, S.92, D.136, V.138 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:V.138 Hydrogen bonds: A:S.91 ACT.10: 3 residues within 4Å: Chain A: T.421, G.422, V.423 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.422 Water bridges: A:F.420, A:F.420, A:V.423 ACT.20: 3 residues within 4Å: Chain B: Y.90, S.92, V.138 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:Y.90, B:V.138 Water bridges: B:S.91 ACT.21: 3 residues within 4Å: Chain B: E.52, Y.90, Q.97 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Y.90, B:Q.97 Water bridges: B:T.55 ACT.22: 3 residues within 4Å: Chain B: Q.79, R.252 Chain C: A.268 6 PLIP interactions: 1 interactions with chain C, 5 interactions with chain B Water bridges: C:A.268, B:Q.79, B:R.80, B:R.252 Hydrogen bonds: B:Q.79 Salt bridges: B:R.252 ACT.23: 3 residues within 4Å: Chain B: Y.95, Y.101, Y.112 1 PLIP interactions: 1 interactions with chain B Water bridges: B:A.96 ACT.36: 5 residues within 4Å: Chain C: Y.90, S.91, S.92, D.136, V.138 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:S.91 Water bridges: C:S.92

4 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.11: 7 residues within 4Å: Chain A: G.124, H.125, S.126, D.259 Chain C: S.107, Q.111 Ligands: GOL.6 4 PLIP interactions: 1 interactions with chain C, 3 interactions with chain A Water bridges: C:K.110, A:H.125, A:D.261 Hydrogen bonds: A:H.125 PEG.24: 7 residues within 4Å: Chain B: C.37, T.154, R.156, I.207, M.208, N.209, C.242 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.156, B:I.207, B:N.209 PEG.37: 8 residues within 4Å: Chain C: E.52, I.53, P.54, T.55, D.56, G.61, Y.90, Q.97 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:T.55, C:D.56, C:D.56, C:Y.90, C:Q.97 PEG.38: 8 residues within 4Å: Chain B: V.432, S.433, T.435 Chain C: G.63, W.65, V.66, P.67, T.68 3 PLIP interactions: 1 interactions with chain C, 2 interactions with chain B Water bridges: C:T.68 Hydrogen bonds: B:S.433, B:S.433

6 x NGA: 2-acetamido-2-deoxy-beta-D-galactopyranose(Post Translational Modification)

NGA.13: 4 residues within 4Å: Chain A: T.429 Chain B: H.290, R.292 Ligands: NGA.14 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:R.292 Water bridges: A:T.429, A:T.429 NGA.14: 8 residues within 4Å: Chain A: T.430, A.431, V.432 Chain B: A.45, T.46, P.67, P.70 Ligands: NGA.13 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Water bridges: A:A.431, A:A.431 Hydrogen bonds: B:T.46 NGA.26: 4 residues within 4Å: Chain B: T.429 Chain C: H.290, R.292 Ligands: NGA.27 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain C Water bridges: B:T.429, B:T.429 Hydrogen bonds: C:R.292 NGA.27: 8 residues within 4Å: Chain B: T.430, A.431, V.432 Chain C: A.45, T.46, P.67, P.70 Ligands: NGA.26 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:T.46, C:T.46 NGA.40: 4 residues within 4Å: Chain A: H.290, R.292 Chain C: T.429 Ligands: NGA.41 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain A Water bridges: C:T.429, C:T.429 Hydrogen bonds: A:R.292 NGA.41: 7 residues within 4Å: Chain A: A.45, T.46, P.70 Chain C: T.430, A.431, V.432 Ligands: NGA.40 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.46

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dubois, R.M. et al., Functional and Evolutionary Insight from the Crystal Structure of Rubella Virus Protein E1. Nature (2013)

Release Date

2013-01-09

Peptides

E1 ENVELOPE GLYCOPROTEIN: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

E1 ENVELOPE GLYCOPROTEIN

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