SMTL ID : 7adt.1

Orf virus Apoptosis inhibitor ORFV125

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.21 Å

Oligo State

hetero-2-2-mer

Ligands

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

EDO.1: 9 residues within 4Å: Chain A: L.22, A.23, Y.26, F.116 Chain C: A.23, Y.26, F.116, V.120 Ligands: EDO.6 No protein-ligand interaction detected (PLIP) EDO.2: 6 residues within 4Å: Chain A: E.25, E.28, A.29, E.32 Chain C: R.105 Ligands: MG.38 5 PLIP interactions: 2 interactions with chain C, 3 interactions with chain A Hydrogen bonds: C:R.105, C:R.105, A:E.25, A:E.25, A:A.29 EDO.5: 5 residues within 4Å: Chain A: E.65, L.106, W.107 Ligands: MG.17, MG.19 No protein-ligand interaction detected (PLIP) EDO.6: 10 residues within 4Å: Chain A: Y.26, V.120, L.124 Chain C: A.19, L.22, A.23, L.113, F.116, M.117 Ligands: EDO.1 No protein-ligand interaction detected (PLIP) EDO.29: 1 residues within 4Å: Chain C: R.39 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:R.39 EDO.30: 1 residues within 4Å: Ligands: MG.39 No protein-ligand interaction detected (PLIP) EDO.31: 2 residues within 4Å: Chain C: T.35, P.36 No protein-ligand interaction detected (PLIP)

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 6 residues within 4Å: Chain A: D.40, E.43, A.44, V.47, A.143, H.146 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.40, A:A.44 GOL.4: 4 residues within 4Å: Chain A: R.53, L.57, Q.102, R.105 4 PLIP interactions: 1 interactions with chain C, 3 interactions with chain A Water bridges: C:E.25, A:R.105 Hydrogen bonds: A:Q.102, A:Q.102

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

MG.7: 3 residues within 4Å: Chain A: A.86, T.88, P.128 No protein-ligand interaction detected (PLIP) MG.8: 2 residues within 4Å: Chain A: V.114, R.118 No protein-ligand interaction detected (PLIP) MG.9: 2 residues within 4Å: Chain A: P.128, A.131 No protein-ligand interaction detected (PLIP) MG.10: 6 residues within 4Å: Chain A: D.132, E.133, G.136, Q.140 Chain C: D.11, I.12 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:D.11 MG.11: 3 residues within 4Å: Chain A: L.42, R.46 Chain C: Y.21 No protein-ligand interaction detected (PLIP) MG.12: 4 residues within 4Å: Chain A: R.46, E.50, R.53 Chain C: Y.21 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A Metal complexes: C:Y.21, A:R.46 MG.13: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.14: 2 residues within 4Å: Chain A: A.86, T.88 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:A.86 MG.15: 3 residues within 4Å: Chain A: D.10, D.11 Ligands: MG.16 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.11 MG.16: 3 residues within 4Å: Chain A: D.10, D.11 Ligands: MG.15 No protein-ligand interaction detected (PLIP) MG.17: 2 residues within 4Å: Chain A: E.65 Ligands: EDO.5 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:E.65 MG.18: 2 residues within 4Å: Chain A: R.111, V.114 No protein-ligand interaction detected (PLIP) MG.19: 3 residues within 4Å: Chain A: N.72, W.107 Ligands: EDO.5 No protein-ligand interaction detected (PLIP) MG.20: 1 residues within 4Å: Chain A: E.85 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:E.85 MG.21: 6 residues within 4Å: Chain A: V.30, Q.33, L.34 Chain C: A.16, T.108, R.109 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:V.30 MG.22: 3 residues within 4Å: Chain A: Q.33 Chain C: T.108, R.109 No protein-ligand interaction detected (PLIP) MG.23: 4 residues within 4Å: Chain A: H.74, I.75, A.78 Chain B: T.7 No protein-ligand interaction detected (PLIP) MG.24: 1 residues within 4Å: Chain A: D.10 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.10 MG.25: 2 residues within 4Å: Chain A: E.65, I.75 No protein-ligand interaction detected (PLIP) MG.26: 3 residues within 4Å: Chain A: E.85, R.92 Chain B: K.15 No protein-ligand interaction detected (PLIP) MG.27: 3 residues within 4Å: Chain B: E.12, K.15, R.16 No protein-ligand interaction detected (PLIP) MG.28: 3 residues within 4Å: Chain A: P.55 Chain B: I.17, E.20 No protein-ligand interaction detected (PLIP) MG.32: 4 residues within 4Å: Chain C: E.85, A.86, R.92 Chain D: K.15 No protein-ligand interaction detected (PLIP) MG.33: 3 residues within 4Å: Chain C: D.125, R.126 Ligands: MG.34 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:D.125 MG.34: 3 residues within 4Å: Chain C: D.125, R.126 Ligands: MG.33 No protein-ligand interaction detected (PLIP) MG.35: 4 residues within 4Å: Chain C: E.31, E.32, L.34, R.39 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:E.31 MG.36: 2 residues within 4Å: Chain C: A.86, T.88 No protein-ligand interaction detected (PLIP) MG.37: 2 residues within 4Å: Chain C: G.110, R.111 No protein-ligand interaction detected (PLIP) MG.38: 6 residues within 4Å: Chain A: E.25 Chain C: R.53, A.101, Q.102, R.105 Ligands: EDO.2 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:E.25 MG.39: 3 residues within 4Å: Chain C: D.10, D.11 Ligands: EDO.30 No protein-ligand interaction detected (PLIP) MG.40: 3 residues within 4Å: Chain C: E.28, A.29, E.32 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:E.32 MG.41: 2 residues within 4Å: Chain C: S.81, R.126 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:S.81 MG.42: 4 residues within 4Å: Chain C: N.72, H.74, I.75, P.76 2 PLIP interactions: 1 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:N.72, H2O.2 MG.43: 2 residues within 4Å: Chain C: R.92 Chain D: D.19 No protein-ligand interaction detected (PLIP) MG.44: 1 residues within 4Å: Chain C: D.10 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:D.10 MG.45: 3 residues within 4Å: Chain C: D.40, Q.140, A.143 No protein-ligand interaction detected (PLIP) MG.46: 2 residues within 4Å: Chain C: H.74, R.118 No protein-ligand interaction detected (PLIP) MG.47: 2 residues within 4Å: Chain D: Q.3, D.4 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:Q.3 MG.48: 2 residues within 4Å: Chain D: K.9, C.13 No protein-ligand interaction detected (PLIP) MG.49: 2 residues within 4Å: Chain D: C.13, R.16 No protein-ligand interaction detected (PLIP) MG.50: 5 residues within 4Å: Chain C: V.145, H.146 Chain D: N.24, L.27, Q.28 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Suraweera, C.D. et al., Crystal structures of ORFV125 provide insight into orf virus-mediated inhibition of apoptosis. Biochem.J. (2020)

Release Date

2021-10-06

Peptides

Apoptosis inhibitor: AC
Apoptosis regulator BAX: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
B

B
U

D
C

Apoptosis inhibitor

Apoptosis regulator BAX

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