SMTL ID : 7a56.1

Schmallenberg Virus Envelope Glycoprotein Gc Fusion Domains in Postfusion Conformation

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

homo-trimer

Ligands

18 x CL: CHLORIDE ION(Non-functional Binders)

CL.1: 8 residues within 4Å: Chain A: A.261, K.262 Chain B: A.261, K.262 Chain C: A.261, K.262 Ligands: CL.15, CL.29 Ligand excluded by PLIP CL.2: 8 residues within 4Å: Chain A: A.261, K.263 Chain B: A.261, K.263 Chain C: A.261, K.263 Ligands: CL.16, CL.30 Ligand excluded by PLIP CL.3: 5 residues within 4Å: Chain A: S.331, S.332 Chain B: K.198, T.232, Q.234 Ligand excluded by PLIP CL.4: 4 residues within 4Å: Chain A: N.314, Y.396, I.411, K.412 Ligand excluded by PLIP CL.5: 3 residues within 4Å: Chain A: P.142, I.143 Chain C: R.297 Ligand excluded by PLIP CL.6: 5 residues within 4Å: Ligands: K.14, CL.20, K.28, CL.34, K.42 Ligand excluded by PLIP CL.15: 8 residues within 4Å: Chain A: A.261, K.262 Chain B: A.261, K.262 Chain C: A.261, K.262 Ligands: CL.1, CL.29 Ligand excluded by PLIP CL.16: 8 residues within 4Å: Chain A: A.261, K.263 Chain B: A.261, K.263 Chain C: A.261, K.263 Ligands: CL.2, CL.30 Ligand excluded by PLIP CL.17: 5 residues within 4Å: Chain B: S.331, S.332 Chain C: K.198, T.232, Q.234 Ligand excluded by PLIP CL.18: 4 residues within 4Å: Chain B: N.314, Y.396, I.411, K.412 Ligand excluded by PLIP CL.19: 3 residues within 4Å: Chain A: R.297 Chain B: P.142, I.143 Ligand excluded by PLIP CL.20: 5 residues within 4Å: Ligands: CL.6, K.14, K.28, CL.34, K.42 Ligand excluded by PLIP CL.29: 8 residues within 4Å: Chain A: A.261, K.262 Chain B: A.261, K.262 Chain C: A.261, K.262 Ligands: CL.1, CL.15 Ligand excluded by PLIP CL.30: 8 residues within 4Å: Chain A: A.261, K.263 Chain B: A.261, K.263 Chain C: A.261, K.263 Ligands: CL.2, CL.16 Ligand excluded by PLIP CL.31: 5 residues within 4Å: Chain A: K.198, T.232, Q.234 Chain C: S.331, S.332 Ligand excluded by PLIP CL.32: 4 residues within 4Å: Chain C: N.314, Y.396, I.411, K.412 Ligand excluded by PLIP CL.33: 3 residues within 4Å: Chain B: R.297 Chain C: P.142, I.143 Ligand excluded by PLIP CL.34: 5 residues within 4Å: Ligands: CL.6, K.14, CL.20, K.28, K.42 Ligand excluded by PLIP

9 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.7: 8 residues within 4Å: Chain A: T.279, D.301 Chain B: T.279, D.301 Chain C: T.279, D.301 Ligands: PO4.21, PO4.35 12 PLIP interactions: 4 interactions with chain C, 4 interactions with chain B, 4 interactions with chain A Hydrogen bonds: C:T.279, C:T.279, C:D.301, B:T.279, B:T.279, B:T.279, A:T.279, A:T.279, A:D.301 Water bridges: C:K.262, B:K.262, A:K.262 PO4.8: 7 residues within 4Å: Chain A: K.154, R.156 Chain B: K.154 Chain C: K.154, R.156 Ligands: PO4.22, PO4.36 16 PLIP interactions: 7 interactions with chain B, 4 interactions with chain A, 5 interactions with chain C Water bridges: B:K.154, B:K.154, B:K.154, B:R.156, B:Y.284, A:K.154, A:R.156, C:K.154, C:K.154, C:R.156 Salt bridges: B:K.154, B:R.156, A:K.154, A:R.156, C:K.154, C:R.156 PO4.9: 3 residues within 4Å: Chain A: Q.197 Chain C: K.390, K.398 7 PLIP interactions: 5 interactions with chain C, 2 interactions with chain A Water bridges: C:K.390, C:K.390, C:S.391, A:K.112 Salt bridges: C:K.390, C:K.398 Hydrogen bonds: A:Q.197 PO4.21: 8 residues within 4Å: Chain A: T.279, D.301 Chain B: T.279, D.301 Chain C: T.279, D.301 Ligands: PO4.7, PO4.35 12 PLIP interactions: 4 interactions with chain B, 4 interactions with chain C, 4 interactions with chain A Hydrogen bonds: B:T.279, B:T.279, B:D.301, C:T.279, C:T.279, C:T.279, A:T.279, A:T.279, A:D.301 Water bridges: B:K.262, C:K.262, A:K.262 PO4.22: 7 residues within 4Å: Chain A: K.154, R.156 Chain B: K.154, R.156 Chain C: K.154 Ligands: PO4.8, PO4.36 16 PLIP interactions: 4 interactions with chain B, 6 interactions with chain A, 6 interactions with chain C Water bridges: B:K.154, B:R.156, A:K.154, A:K.154, A:K.154, A:R.156, C:K.154, C:K.154, C:R.156, C:Y.284 Salt bridges: B:K.154, B:R.156, A:K.154, A:R.156, C:K.154, C:R.156 PO4.23: 3 residues within 4Å: Chain A: K.390, K.398 Chain B: Q.197 7 PLIP interactions: 5 interactions with chain A, 2 interactions with chain B Water bridges: A:K.390, A:K.390, A:S.391, B:K.112 Salt bridges: A:K.390, A:K.398 Hydrogen bonds: B:Q.197 PO4.35: 8 residues within 4Å: Chain A: T.279, D.301 Chain B: T.279, D.301 Chain C: T.279, D.301 Ligands: PO4.7, PO4.21 12 PLIP interactions: 4 interactions with chain C, 4 interactions with chain B, 4 interactions with chain A Hydrogen bonds: C:T.279, C:T.279, C:D.301, B:T.279, B:T.279, B:D.301, A:T.279, A:T.279, A:T.279 Water bridges: C:K.262, B:K.262, A:K.262 PO4.36: 7 residues within 4Å: Chain A: K.154 Chain B: K.154, R.156 Chain C: K.154, R.156 Ligands: PO4.8, PO4.22 16 PLIP interactions: 5 interactions with chain B, 7 interactions with chain A, 4 interactions with chain C Water bridges: B:K.154, B:K.154, B:R.156, A:K.154, A:K.154, A:K.154, A:R.156, A:Y.284, C:K.154, C:R.156 Salt bridges: B:K.154, B:R.156, A:K.154, A:R.156, C:K.154, C:R.156 PO4.37: 3 residues within 4Å: Chain B: K.390, K.398 Chain C: Q.197 7 PLIP interactions: 2 interactions with chain C, 5 interactions with chain B Hydrogen bonds: C:Q.197 Water bridges: C:K.112, B:K.390, B:K.390, B:S.391 Salt bridges: B:K.390, B:K.398

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

NA.10: 1 residues within 4Å: Chain A: Y.42 No protein-ligand interaction detected (PLIP) NA.11: 2 residues within 4Å: Chain A: W.160, A.288 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:W.160, A:G.161 NA.12: 1 residues within 4Å: Chain A: W.165 No protein-ligand interaction detected (PLIP) NA.13: 1 residues within 4Å: Chain A: Y.350 No protein-ligand interaction detected (PLIP) NA.24: 1 residues within 4Å: Chain B: Y.42 No protein-ligand interaction detected (PLIP) NA.25: 2 residues within 4Å: Chain B: W.160, A.288 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:W.160, B:G.161 NA.26: 1 residues within 4Å: Chain B: W.165 No protein-ligand interaction detected (PLIP) NA.27: 1 residues within 4Å: Chain B: Y.350 1 PLIP interactions: 1 interactions with chain B Water bridges: B:N.90 NA.38: 1 residues within 4Å: Chain C: Y.42 No protein-ligand interaction detected (PLIP) NA.39: 2 residues within 4Å: Chain C: W.160, A.288 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:W.160, C:G.161 NA.40: 1 residues within 4Å: Chain C: W.165 No protein-ligand interaction detected (PLIP) NA.41: 1 residues within 4Å: Chain C: Y.350 1 PLIP interactions: 1 interactions with chain C Water bridges: C:N.90

3 x K: POTASSIUM ION(Non-covalent)

K.14: 4 residues within 4Å: Chain A: W.160 Ligands: CL.6, CL.20, CL.34 No protein-ligand interaction detected (PLIP) K.28: 4 residues within 4Å: Chain B: W.160 Ligands: CL.6, CL.20, CL.34 No protein-ligand interaction detected (PLIP) K.42: 4 residues within 4Å: Chain C: W.160 Ligands: CL.6, CL.20, CL.34 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hellert, J. et al., Structure, function, and evolution of the Orthobunyavirus membrane fusion glycoprotein. Cell Rep (2023)

Release Date

2021-09-01

Peptides

Envelopment polyprotein: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

Envelopment polyprotein