SMTL ID : 7ads.1

Orf virus Apoptosis inhibitor ORFV125

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.22 Å

Oligo State

homo-dimer

Ligands

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

EDO.1: 3 residues within 4Å: Chain A: P.36, D.40 Ligands: NA.8 No protein-ligand interaction detected (PLIP) EDO.2: 6 residues within 4Å: Chain A: L.83, S.89, G.91, R.92, T.95 Ligands: EDO.5 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.89, A:T.95 Water bridges: A:R.53 EDO.3: 6 residues within 4Å: Chain A: T.88, S.89, P.90, P.128, T.130, D.134 No protein-ligand interaction detected (PLIP) EDO.4: 3 residues within 4Å: Chain A: G.64, E.65, Q.112 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.65 EDO.5: 8 residues within 4Å: Chain A: S.48, R.53, G.91, V.94, T.95, W.138, V.142 Ligands: EDO.2 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.53, A:R.53, A:T.95, A:W.138 Water bridges: A:S.48, A:T.95 EDO.6: 5 residues within 4Å: Chain A: Y.21, E.25, E.28 Chain B: R.46, R.105 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.25 Water bridges: A:E.28 EDO.7: 9 residues within 4Å: Chain A: Q.33, L.34, T.35, E.38 Chain B: D.13, A.16, T.108, R.109, G.110 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.38 EDO.19: 3 residues within 4Å: Chain B: P.36, D.40 Ligands: NA.26 No protein-ligand interaction detected (PLIP) EDO.20: 6 residues within 4Å: Chain B: L.83, S.89, G.91, R.92, T.95 Ligands: EDO.23 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.89, B:T.95 Water bridges: B:R.53 EDO.21: 6 residues within 4Å: Chain B: T.88, S.89, P.90, P.128, T.130, D.134 No protein-ligand interaction detected (PLIP) EDO.22: 3 residues within 4Å: Chain B: G.64, E.65, Q.112 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.65 EDO.23: 8 residues within 4Å: Chain B: S.48, R.53, G.91, V.94, T.95, W.138, V.142 Ligands: EDO.20 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:R.53, B:R.53, B:T.95, B:W.138 Water bridges: B:S.48, B:T.95 EDO.24: 5 residues within 4Å: Chain A: R.46, R.105 Chain B: Y.21, E.25, E.28 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.25 EDO.25: 9 residues within 4Å: Chain A: D.13, A.16, T.108, R.109, G.110 Chain B: Q.33, L.34, T.35, E.38 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.38

10 x NA: SODIUM ION(Non-functional Binders)

NA.8: 4 residues within 4Å: Chain A: P.36, R.37, D.40 Ligands: EDO.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.40 NA.9: 3 residues within 4Å: Chain A: S.15, G.110, R.111 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.15, A:S.15 NA.10: 3 residues within 4Å: Chain A: S.54, L.56, L.79 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.54 NA.11: 5 residues within 4Å: Chain A: L.84, T.88, R.126, L.127, P.128 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:L.84 NA.12: 3 residues within 4Å: Chain A: V.142, V.145, H.146 No protein-ligand interaction detected (PLIP) NA.26: 4 residues within 4Å: Chain B: P.36, R.37, D.40 Ligands: EDO.19 No protein-ligand interaction detected (PLIP) NA.27: 3 residues within 4Å: Chain B: S.15, G.110, R.111 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.15, B:G.110 NA.28: 3 residues within 4Å: Chain B: S.54, L.56, L.79 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.54 NA.29: 5 residues within 4Å: Chain B: L.84, T.88, R.126, L.127, P.128 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:L.127 NA.30: 3 residues within 4Å: Chain B: V.142, V.145, H.146 No protein-ligand interaction detected (PLIP)

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

CL.13: 3 residues within 4Å: Chain A: V.52, Q.102, R.105 Ligand excluded by PLIP CL.14: 2 residues within 4Å: Chain A: A.143, G.147 Ligand excluded by PLIP CL.31: 3 residues within 4Å: Chain B: V.52, Q.102, R.105 Ligand excluded by PLIP CL.32: 2 residues within 4Å: Chain B: A.143, G.147 Ligand excluded by PLIP

8 x MG: MAGNESIUM ION(Non-covalent)

MG.15: 3 residues within 4Å: Chain A: Q.33, T.35 Chain B: R.9 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:Q.33 MG.16: 7 residues within 4Å: Chain A: V.52, R.53, S.54, L.57, Q.58, L.99, Q.102 No protein-ligand interaction detected (PLIP) MG.17: 3 residues within 4Å: Chain A: H.74, I.75, A.78 No protein-ligand interaction detected (PLIP) MG.18: 5 residues within 4Å: Chain A: M.117, Y.121 Chain B: M.117, Y.121 Ligands: MG.36 No protein-ligand interaction detected (PLIP) MG.33: 3 residues within 4Å: Chain A: R.9 Chain B: Q.33, T.35 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:Q.33 MG.34: 7 residues within 4Å: Chain B: V.52, R.53, S.54, L.57, Q.58, L.99, Q.102 No protein-ligand interaction detected (PLIP) MG.35: 3 residues within 4Å: Chain B: H.74, I.75, A.78 No protein-ligand interaction detected (PLIP) MG.36: 5 residues within 4Å: Chain A: M.117, Y.121 Chain B: M.117, Y.121 Ligands: MG.18 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: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Apoptosis inhibitor

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