SMTL ID : 6cj6.3 (3 other biounits)

Structure of the poxvirus protein F9

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

monomer

Ligands

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

PG0.1: 5 residues within 4Å: Chain A: A.111, E.112, I.116 Ligands: EDO.12, GOL.17 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.112, A:I.116 PG0.2: 4 residues within 4Å: Chain A: D.16, Q.138 Ligands: EOH.25, PGE.39 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.138

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

PEG.3: 9 residues within 4Å: Chain A: T.32, A.34, M.56, G.143, S.144, A.145, E.146 Ligands: EDO.12, GOL.17 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.32, A:A.34, A:I.116, A:A.145 Water bridges: A:T.32 PEG.4: 4 residues within 4Å: Chain A: A.99, V.100, K.105 Ligands: PDO.21 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:V.100, A:K.105 PEG.5: 5 residues within 4Å: Chain A: R.83, D.94 Ligands: GOL.19, PDO.20, EOH.26 No protein-ligand interaction detected (PLIP) PEG.6: 3 residues within 4Å: Chain A: E.39, K.121 Ligands: MOH.33 1 PLIP interactions: 1 interactions with chain A Water bridges: A:K.121

1 x P33: 3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL(Non-covalent)

P33.7: 9 residues within 4Å: Chain A: L.13, D.16, S.17, Q.20, K.21, Q.24, E.72, L.76 Ligands: PGE.39 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.21, A:Q.24

1 x ETE: 2-{2-[2-2-(METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL(Non-covalent)

ETE.8: 5 residues within 4Å: Chain A: C.33, H.36, D.118 Ligands: EDO.9, EOH.31 No protein-ligand interaction detected (PLIP)

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

EDO.9: 3 residues within 4Å: Chain A: C.33, A.34 Ligands: ETE.8 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.118 EDO.10: 3 residues within 4Å: Chain A: I.85, E.88, S.157 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.88, A:E.88 EDO.11: 2 residues within 4Å: Chain A: V.163, P.164 No protein-ligand interaction detected (PLIP) EDO.12: 3 residues within 4Å: Chain A: A.34 Ligands: PG0.1, PEG.3 No protein-ligand interaction detected (PLIP) EDO.13: 1 residues within 4Å: Chain A: E.126 No protein-ligand interaction detected (PLIP) EDO.14: 5 residues within 4Å: Chain A: S.75, L.76, L.77, P.78, R.82 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.77, A:R.82 EDO.15: 1 residues within 4Å: Chain A: E.112 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.112

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.16: 1 residues within 4Å: Chain A: A.23 No protein-ligand interaction detected (PLIP) GOL.17: 5 residues within 4Å: Chain A: S.59, S.144, E.146 Ligands: PG0.1, PEG.3 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.59 Water bridges: A:S.59 GOL.18: 4 residues within 4Å: Chain A: R.83, A.84, E.87 Ligands: EOH.29 No protein-ligand interaction detected (PLIP) GOL.19: 1 residues within 4Å: Ligands: PEG.5 No protein-ligand interaction detected (PLIP)

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

PDO.20: 3 residues within 4Å: Chain A: E.87 Ligands: PEG.5, EOH.26 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.87 PDO.21: 7 residues within 4Å: Chain A: D.92, D.95, V.100, S.101, K.102, K.105 Ligands: PEG.4 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:V.100 Water bridges: A:K.102

10 x EOH: ETHANOL(Non-functional Binders)

EOH.22: 1 residues within 4Å: Chain A: S.26 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.26, A:S.26 EOH.23: 4 residues within 4Å: Chain A: Q.43, G.125, E.126, K.160 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.126, A:K.160 EOH.24: 2 residues within 4Å: Chain A: K.5, E.6 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:K.5 Hydrogen bonds: A:E.6 EOH.25: 3 residues within 4Å: Chain A: E.6, D.16 Ligands: PG0.2 No protein-ligand interaction detected (PLIP) EOH.26: 4 residues within 4Å: Chain A: D.92, D.94 Ligands: PEG.5, PDO.20 No protein-ligand interaction detected (PLIP) EOH.27: 4 residues within 4Å: Chain A: K.5, K.8, V.163, P.164 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:V.163 EOH.28: 3 residues within 4Å: Chain A: A.129, P.130, P.131 No protein-ligand interaction detected (PLIP) EOH.29: 3 residues within 4Å: Chain A: E.87, E.88 Ligands: GOL.18 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.88 EOH.30: 1 residues within 4Å: Chain A: E.79 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.79 EOH.31: 3 residues within 4Å: Chain A: D.118, I.119 Ligands: ETE.8 1 PLIP interactions: 1 interactions with chain A Water bridges: A:D.118

6 x MOH: METHANOL(Non-functional Binders)

MOH.32: 3 residues within 4Å: Chain A: D.16, L.19, Q.20 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.20 MOH.33: 3 residues within 4Å: Chain A: Y.110, N.114 Ligands: PEG.6 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.110 MOH.34: 2 residues within 4Å: Chain A: K.21, E.72 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.21, A:K.21 MOH.35: 1 residues within 4Å: Chain A: K.54 No protein-ligand interaction detected (PLIP) MOH.36: 1 residues within 4Å: Chain A: D.118 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.118 MOH.37: 1 residues within 4Å: Chain A: I.119 No protein-ligand interaction detected (PLIP)

1 x PGO: S-1,2-PROPANEDIOL(Non-covalent)

PGO.38: 1 residues within 4Å: Chain A: N.115 No protein-ligand interaction detected (PLIP)

3 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.39: 4 residues within 4Å: Chain A: Q.20, E.72 Ligands: PG0.2, P33.7 No protein-ligand interaction detected (PLIP) PGE.40: 1 residues within 4Å: Chain A: P.131 No protein-ligand interaction detected (PLIP) PGE.41: 4 residues within 4Å: Chain A: V.31, C.33, H.36, N.53 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.53

1 x ETX: 2-ETHOXYETHANOL(Non-covalent)

ETX.42: 1 residues within 4Å: Chain A: K.80 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:K.80

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Diesterbeck, U.S. et al., The 2.1 angstrom structure of protein F9 and its comparison to L1, two components of the conserved poxvirus entry-fusion complex. Sci Rep (2018)

Release Date

2019-03-06

Peptides

Protein F9: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

Protein F9

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