SMTL ID : 5yzd.1

Crystal structure of the prefusion form of measles virus fusion protein in complex with a fusion inhibitor peptide (FIP)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.64 Å

Oligo State

hetero-3-3-mer

Ligands

3 x PHQ- DPN- PHE- GLY: peptide CBZ-DPN-PHE-GLY(Non-covalent)

PHQ-DPN-PHE-GLY.1: 17 residues within 4Å: Chain B: Q.197, L.258, P.339, I.340, S.341, V.347, N.350, N.353, A.354, K.357 Chain D: S.240, P.241 Chain F: G.348, L.351, G.352, I.355, E.359 18 PLIP interactions: 11 interactions with chain B, 6 interactions with chain F, 1 interactions with chain D Hydrophobic interactions: B:L.258, B:P.339, B:I.340, B:I.340, B:V.347, B:N.350, B:N.353, B:A.354, F:L.351, F:L.351, F:I.355, F:I.355, F:I.355, F:I.355, D:P.241 Hydrogen bonds: B:P.339, B:N.350 pi-Stacking: B:W.199 PHQ-DPN-PHE-GLY.4: 17 residues within 4Å: Chain B: G.348, L.351, G.352, I.355, E.359 Chain D: Q.197, L.258, P.339, I.340, S.341, V.347, N.350, N.353, A.354, K.357 Chain F: S.240, P.241 18 PLIP interactions: 6 interactions with chain B, 11 interactions with chain D, 1 interactions with chain F Hydrophobic interactions: B:L.351, B:L.351, B:I.355, B:I.355, B:I.355, B:I.355, D:L.258, D:P.339, D:I.340, D:I.340, D:V.347, D:N.350, D:N.353, D:A.354, F:P.241 Hydrogen bonds: D:P.339, D:N.350 pi-Stacking: D:W.199 PHQ-DPN-PHE-GLY.7: 17 residues within 4Å: Chain B: S.240, P.241 Chain D: G.348, L.351, G.352, I.355, E.359 Chain F: Q.197, L.258, P.339, I.340, S.341, V.347, N.350, N.353, A.354, K.357 18 PLIP interactions: 6 interactions with chain D, 11 interactions with chain F, 1 interactions with chain B Hydrophobic interactions: D:L.351, D:L.351, D:I.355, D:I.355, D:I.355, D:I.355, F:L.258, F:P.339, F:I.340, F:I.340, F:V.347, F:N.350, F:N.353, F:A.354, B:P.241 Hydrogen bonds: F:P.339, F:N.350 pi-Stacking: F:W.199

3 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.2: 8 residues within 4Å: Chain A: H.8, N.11 Chain B: G.249, S.250, T.251, R.333, I.334, D.335 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.335 NAG-NAG.5: 8 residues within 4Å: Chain C: H.8, N.11 Chain D: G.249, S.250, T.251, R.333, I.334, D.335 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:D.335 NAG-NAG.8: 8 residues within 4Å: Chain E: H.8, N.11 Chain F: G.249, S.250, T.251, R.333, I.334, D.335 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:D.335

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

NAG.3: 6 residues within 4Å: Chain A: N.43, T.45 Chain B: E.43, T.44, T.45, N.46 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:E.43, A:T.45 NAG.6: 6 residues within 4Å: Chain C: N.43, T.45 Chain D: E.43, T.44, T.45, N.46 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:T.45, C:T.45, D:E.43 NAG.9: 6 residues within 4Å: Chain E: N.43, T.45 Chain F: E.43, T.44, T.45, N.46 2 PLIP interactions: 1 interactions with chain E, 1 interactions with chain F Hydrogen bonds: E:T.45, F:E.43

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hashiguchi, T. et al., Structures of the prefusion form of measles virus fusion protein in complex with inhibitors. Proc. Natl. Acad. Sci. U.S.A. (2018)

Release Date

2018-02-21

Peptides

glycoprotein F2: ACE
glycoprotein F1,measles virus fusion protein: BDF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
A

E
A

B
C

D
C

F
C

glycoprotein F2

glycoprotein F1,measles virus fusion protein

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