SMTL ID : 7p9w.1

Epstein-Barr virus encoded apoptosis regulator BHRF1 in complex with Puma BH3

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

hetero-1-1-mer

Ligands

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

PO4.1: 4 residues within 4Å: Chain A: H.123, R.126, T.127, C.130 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.127 Water bridges: A:R.126, A:R.126 PO4.2: 4 residues within 4Å: Chain A: H.39, P.40, Y.136 Ligands: EDO.4 3 PLIP interactions: 3 interactions with chain A Water bridges: A:H.39, A:H.39 Salt bridges: A:H.39 PO4.3: 2 residues within 4Å: Chain A: S.54, P.55 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.54

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

EDO.4: 4 residues within 4Å: Chain A: P.135, Y.136, Y.137 Ligands: PO4.2 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.136 EDO.5: 8 residues within 4Å: Chain A: H.33, G.34, N.35, G.36, T.37, C.129, C.130, Q.132 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.35 Water bridges: A:G.36, A:T.37 EDO.6: 4 residues within 4Å: Chain A: R.62, V.65, L.66, I.167 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.62, A:R.62, A:R.62 EDO.7: 6 residues within 4Å: Chain A: I.86, L.128, T.134, P.135, V.138 Ligands: MG.14 No protein-ligand interaction detected (PLIP) EDO.10: 5 residues within 4Å: Chain A: H.105, R.106, R.113 Chain B: R.13 Ligands: MG.16 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.106, A:R.113, A:R.113 EDO.23: 5 residues within 4Å: Chain B: Q.3, R.6, E.7, A.10, R.14 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.6

1 x NH4: AMMONIUM ION(Non-functional Binders)

NH4.8: 3 residues within 4Å: Chain A: S.110, L.111, W.156 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:L.111

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

PDO.9: 7 residues within 4Å: Chain A: S.17, R.19, E.20, T.49, P.50, E.151, D.154 No protein-ligand interaction detected (PLIP) PDO.11: 6 residues within 4Å: Chain A: N.97, F.100, E.148, A.149, E.151, G.152 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.148, A:G.152

5 x MG: MAGNESIUM ION(Non-covalent)(Non-functional Binders)

MG.12: 4 residues within 4Å: Chain A: R.28, R.31, P.55, E.56 No protein-ligand interaction detected (PLIP) MG.13: 3 residues within 4Å: Chain A: R.19, R.144, E.148 No protein-ligand interaction detected (PLIP) MG.14: 6 residues within 4Å: Chain A: W.82, I.86, T.127, L.128, T.134 Ligands: EDO.7 No protein-ligand interaction detected (PLIP) MG.15: 6 residues within 4Å: Chain A: I.103, F.104, H.105, R.106, P.109, R.113 No protein-ligand interaction detected (PLIP) MG.16: 1 residues within 4Å: Ligands: EDO.10 No protein-ligand interaction detected (PLIP)

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

CL.17: 3 residues within 4Å: Chain A: I.71, E.72, S.75 Ligand excluded by PLIP CL.18: 3 residues within 4Å: Chain A: S.75, E.76, T.79 Ligand excluded by PLIP CL.19: 5 residues within 4Å: Chain A: E.90, H.91, V.92, Y.137, L.141 Ligand excluded by PLIP CL.20: 3 residues within 4Å: Chain A: I.70, R.73, N.74 Ligand excluded by PLIP CL.21: 4 residues within 4Å: Chain A: H.33, H.64, E.68, R.126 Ligand excluded by PLIP CL.22: 5 residues within 4Å: Chain A: A.15, Y.16, G.162, W.163, S.164 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Suraweera, C.D. et al., Crystal Structures of Epstein-Barr Virus Bcl-2 Homolog BHRF1 Bound to Bid and Puma BH3 Motif Peptides. Viruses (2022)

Release Date

2022-08-10

Peptides

Apoptosis regulator BHRF1: A
Bcl-2-binding component 3, isoforms 1/2: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Apoptosis regulator BHRF1

Bcl-2-binding component 3, isoforms 1/2

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