SMTL ID : 6cj6.1 (3 other biounits)

Structure of the poxvirus protein F9

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

monomer

Ligands

2 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.1: 4 residues within 4Å: Chain A: E.6, K.8, D.16 Ligands: EOH.27 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.8 PG4.2: 4 residues within 4Å: Chain A: A.2, P.131, G.132 Ligands: EOH.29 No protein-ligand interaction detected (PLIP)

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

PG0.3: 4 residues within 4Å: Chain A: E.87, K.102 Ligands: EDO.15, EOH.38 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.87 PG0.4: 4 residues within 4Å: Chain A: Y.110, N.114, Q.120, K.121 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.110, A:N.114, A:K.121 PG0.5: 3 residues within 4Å: Chain A: R.83, D.94 Ligands: EDO.14 No protein-ligand interaction detected (PLIP) PG0.6: 3 residues within 4Å: Chain A: E.87, E.88 Ligands: PDO.22 No protein-ligand interaction detected (PLIP)

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

PEG.7: 3 residues within 4Å: Chain A: E.3, T.4 Ligands: PDO.19 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.4, A:T.4 PEG.8: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

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

EDO.9: 2 residues within 4Å: Chain A: T.4, N.46 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.4 EDO.10: 5 residues within 4Å: Chain A: Q.43, G.125, K.156 Ligands: GOL.18, EOH.26 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.43, A:K.156 EDO.11: 1 residues within 4Å: Chain A: N.30 No protein-ligand interaction detected (PLIP) EDO.12: 2 residues within 4Å: Chain A: C.33, H.36 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.36 EDO.13: 3 residues within 4Å: Chain A: K.80, D.81, A.84 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.80 EDO.14: 3 residues within 4Å: Chain A: R.83 Ligands: PG0.5, PDO.24 No protein-ligand interaction detected (PLIP) EDO.15: 2 residues within 4Å: Ligands: PG0.3, EOH.38 No protein-ligand interaction detected (PLIP) EDO.16: 3 residues within 4Å: Chain A: N.58, S.59, R.60 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.58, A:S.59, A:S.59, A:R.60 EDO.17: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.18: 3 residues within 4Å: Chain A: I.41, G.42 Ligands: EDO.10 No protein-ligand interaction detected (PLIP)

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

PDO.19: 2 residues within 4Å: Chain A: E.3 Ligands: PEG.7 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.3 PDO.20: 4 residues within 4Å: Chain A: S.17, Q.20, K.21, E.72 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.20, A:K.21 PDO.21: 4 residues within 4Å: Chain A: K.105, N.108, A.109, E.112 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:N.108 Hydrogen bonds: A:K.105, A:E.112 Water bridges: A:N.108, A:N.108 PDO.22: 4 residues within 4Å: Chain A: E.88, S.157 Ligands: PG0.6, EOH.26 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:E.88 PDO.23: 3 residues within 4Å: Chain A: D.92, D.94, D.95 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.95 PDO.24: 2 residues within 4Å: Chain A: K.80 Ligands: EDO.14 No protein-ligand interaction detected (PLIP) PDO.25: 3 residues within 4Å: Chain A: L.19, T.52, K.54 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.52, A:K.54 Water bridges: A:Q.138

13 x EOH: ETHANOL(Non-functional Binders)

EOH.26: 4 residues within 4Å: Chain A: K.156, K.160 Ligands: EDO.10, PDO.22 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.160, A:K.160 EOH.27: 2 residues within 4Å: Ligands: PG4.1, PGO.47 No protein-ligand interaction detected (PLIP) EOH.28: 1 residues within 4Å: Chain A: A.34 No protein-ligand interaction detected (PLIP) EOH.29: 3 residues within 4Å: Chain A: E.3, G.132 Ligands: PG4.2 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.132 EOH.30: 2 residues within 4Å: Ligands: EOH.31, ETX.51 No protein-ligand interaction detected (PLIP) EOH.31: 2 residues within 4Å: Ligands: EOH.30, MOH.44 No protein-ligand interaction detected (PLIP) EOH.32: 3 residues within 4Å: Chain A: P.164, P.165 Ligands: ETX.51 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:P.165 EOH.33: 2 residues within 4Å: Chain A: V.96 Ligands: EOH.34 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:V.96 EOH.34: 3 residues within 4Å: Chain A: D.95, V.96 Ligands: EOH.33 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:V.96 Hydrogen bonds: A:V.96 EOH.35: 2 residues within 4Å: Chain A: A.99, V.100 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:V.100 Water bridges: A:K.105 EOH.36: 9 residues within 4Å: Chain A: V.67, I.91, D.92, D.95, V.96, P.97, A.99, S.101 Ligands: MOH.42 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:V.67, A:D.95 EOH.37: 6 residues within 4Å: Chain A: S.26, I.27, P.28, V.31, M.56, S.57 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:V.31 Hydrogen bonds: A:I.27 EOH.38: 3 residues within 4Å: Ligands: PG0.3, EDO.15, PGO.49 No protein-ligand interaction detected (PLIP)

8 x MOH: METHANOL(Non-functional Binders)

MOH.39: 2 residues within 4Å: Chain A: K.121, Q.152 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.121, A:Q.152 MOH.40: 1 residues within 4Å: Chain A: G.38 No protein-ligand interaction detected (PLIP) MOH.41: 7 residues within 4Å: Chain A: Y.18, M.66, V.140, T.142, A.147, N.148, L.151 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.142, A:A.147 MOH.42: 9 residues within 4Å: Chain A: R.60, F.63, V.67, P.97, A.99, V.100, S.101, E.104 Ligands: EOH.36 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.60, A:S.101, A:S.101, A:E.104 MOH.43: 1 residues within 4Å: Chain A: I.119 No protein-ligand interaction detected (PLIP) MOH.44: 1 residues within 4Å: Ligands: EOH.31 No protein-ligand interaction detected (PLIP) MOH.45: 4 residues within 4Å: Chain A: A.111, E.112, N.114, I.116 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.112, A:I.116 MOH.46: 1 residues within 4Å: Chain A: E.146 No protein-ligand interaction detected (PLIP)

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

PGO.47: 3 residues within 4Å: Chain A: K.8 Ligands: EOH.27, ETX.50 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.8 PGO.48: 2 residues within 4Å: Chain A: H.36, I.119 No protein-ligand interaction detected (PLIP) PGO.49: 6 residues within 4Å: Chain A: G.90, I.91, D.92, S.101, K.102 Ligands: EOH.38 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:D.92 Hydrogen bonds: A:K.102

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

ETX.50: 2 residues within 4Å: Chain A: I.166 Ligands: PGO.47 2 PLIP interactions: 2 interactions with chain A Water bridges: A:K.8, A:K.8 ETX.51: 4 residues within 4Å: Chain A: P.165, I.166 Ligands: EOH.30, EOH.32 No protein-ligand interaction detected (PLIP)

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
A

Protein F9

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