SMTL ID : 4mmu.1

Crystal Structure of Prefusion-stabilized RSV F Variant DS-Cav1 at pH 5.5

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.00 Å

Oligo State

hetero-3-3-mer

Ligands

12 x SO4: SULFATE ION(Non-functional Binders)

SO4.1: 6 residues within 4Å: Chain B: F.1, R.203, Q.218, E.220 Chain E: R.81, A.82 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:F.1, B:Q.218 Salt bridges: B:R.203 SO4.3: 5 residues within 4Å: Chain B: S.307, K.309, G.328, K.329, S.330 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.307, B:S.330 SO4.4: 4 residues within 4Å: Chain B: N.39, L.57, D.58, K.90 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:N.39, B:L.57, B:D.58 Water bridges: B:N.39 Salt bridges: B:K.90 SO4.5: 4 residues within 4Å: Chain B: I.156, K.157, E.158, E.159 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.159 SO4.7: 6 residues within 4Å: Chain A: R.81, A.82 Chain D: F.1, R.203, Q.218, E.220 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:F.1, D:Q.218 Salt bridges: D:R.203 SO4.9: 5 residues within 4Å: Chain D: S.307, K.309, G.328, K.329, S.330 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:S.307, D:S.330 SO4.10: 4 residues within 4Å: Chain D: N.39, L.57, D.58, K.90 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:N.39, D:L.57, D:D.58 Water bridges: D:N.39 Salt bridges: D:K.90 SO4.11: 4 residues within 4Å: Chain D: I.156, K.157, E.158, E.159 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:E.159 SO4.13: 6 residues within 4Å: Chain C: R.81, A.82 Chain F: F.1, R.203, Q.218, E.220 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:F.1, F:Q.218 Salt bridges: F:R.203 SO4.15: 5 residues within 4Å: Chain F: S.307, K.309, G.328, K.329, S.330 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:S.307, F:S.330 SO4.16: 4 residues within 4Å: Chain F: N.39, L.57, D.58, K.90 5 PLIP interactions: 5 interactions with chain F Hydrogen bonds: F:N.39, F:L.57, F:D.58 Water bridges: F:N.39 Salt bridges: F:K.90 SO4.17: 4 residues within 4Å: Chain F: I.156, K.157, E.158, E.159 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:E.159

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

NAG.2: 1 residues within 4Å: Chain B: N.364 No protein-ligand interaction detected (PLIP) NAG.8: 1 residues within 4Å: Chain D: N.364 No protein-ligand interaction detected (PLIP) NAG.14: 1 residues within 4Å: Chain F: N.364 No protein-ligand interaction detected (PLIP)

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

PO4.6: 6 residues within 4Å: Chain A: K.17, G.18, Y.19 Chain B: P.176, C.177, W.178 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:G.18, A:Y.19, B:C.177, B:C.177 PO4.12: 6 residues within 4Å: Chain C: K.17, G.18, Y.19 Chain D: P.176, C.177, W.178 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:G.18, C:Y.19, D:C.177, D:C.177 PO4.18: 6 residues within 4Å: Chain E: K.17, G.18, Y.19 Chain F: P.176, C.177, W.178 4 PLIP interactions: 2 interactions with chain E, 2 interactions with chain F Hydrogen bonds: E:G.18, E:Y.19, F:C.177, F:C.177

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

McLellan, J.S. et al., Structure-based design of a fusion glycoprotein vaccine for respiratory syncytial virus. Science (2013)

Release Date

2013-11-20

Peptides

Fusion glycoprotein F2: ACE
Fusion glycoprotein F1 fused with Fibritin trimerization domain: BDF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
A

E
A

B
B

D
B

F
B

Fusion glycoprotein F2

Fusion glycoprotein F1 fused with Fibritin trimerization domain

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