- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.86 Å
- Oligo State
- hetero-1-1-mer
- Ligands
- 3 x MG: MAGNESIUM ION(Non-covalent)
- 6 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)
EDO.4: 3 residues within 4Å:- Chain A: N.115, P.116, K.117
2 PLIP interactions:2 interactions with chain A- Hydrogen bonds: A:N.115
- Water bridges: A:N.115
EDO.5: 6 residues within 4Å:- Chain A: L.238, L.239, Q.241, Y.268, R.272
- Ligands: MG.3
3 PLIP interactions:3 interactions with chain A- Hydrogen bonds: A:L.238, A:Y.268, A:R.272
EDO.6: 5 residues within 4Å:- Chain A: L.13, T.65, A.68, R.69, T.335
1 PLIP interactions:1 interactions with chain A- Hydrogen bonds: A:T.335
EDO.7: 3 residues within 4Å:- Chain A: Q.128, F.129
- Ligands: ACT.10
1 PLIP interactions:1 interactions with chain A- Hydrogen bonds: A:F.129
EDO.8: 6 residues within 4Å:- Chain A: G.103, A.104, I.257
- Chain B: P.1, S.4
- Ligands: AR6.18
No protein-ligand interaction detected (PLIP)EDO.9: 4 residues within 4Å:- Chain A: F.122, R.126, L.162, Q.165
1 PLIP interactions:1 interactions with chain A- Hydrogen bonds: A:R.126
- 8 x ACT: ACETATE ION(Non-functional Binders)
ACT.10: 4 residues within 4Å:- Chain A: A.127, F.129, N.130
- Ligands: EDO.7
2 PLIP interactions:2 interactions with chain A- Hydrogen bonds: A:F.129, A:N.130
ACT.11: 4 residues within 4Å:- Chain A: F.129, N.130, K.132
- Ligands: AR6.18
2 PLIP interactions:2 interactions with chain A- Hydrophobic interactions: A:N.130, A:K.132
ACT.12: 2 residues within 4Å:- Chain A: P.281, S.282
2 PLIP interactions:2 interactions with chain A- Hydrogen bonds: A:S.282
- Water bridges: A:A.283
ACT.13: 1 residues within 4Å:- Chain A: N.130
1 PLIP interactions:1 interactions with chain A- Hydrogen bonds: A:N.130
ACT.14: 1 residues within 4Å:- Chain A: K.199
1 PLIP interactions:1 interactions with chain A- Salt bridges: A:K.199
ACT.15: 7 residues within 4Å:- Chain A: R.231, V.250, S.251, E.252, L.253, G.254, E.261
3 PLIP interactions:3 interactions with chain A- Hydrogen bonds: A:V.250
- Salt bridges: A:R.231, A:K.234
ACT.16: 4 residues within 4Å:- Chain A: Q.154, Q.157, K.158, R.161
4 PLIP interactions:4 interactions with chain A- Hydrophobic interactions: A:Q.157
- Hydrogen bonds: A:Q.154, A:K.158
- Salt bridges: A:R.161
ACT.17: 4 residues within 4Å:- Chain A: R.126, G.131, K.132, A.169
2 PLIP interactions:2 interactions with chain A- Hydrophobic interactions: A:R.126
- Hydrogen bonds: A:R.126
- 1 x AR6: [(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL [HYDROXY-[[(2R,3S,4R,5S)-3,4,5-TRIHYDROXYOXOLAN-2-YL]METHOXY]PHOSPHORYL] HYDROGEN PHOSPHATE(Non-covalent)
AR6.18: 25 residues within 4Å:- Chain A: D.63, D.64, G.101, G.103, A.104, G.105, V.106, F.129, G.133, S.134, Y.135, G.136, N.137, G.138, H.168, I.257, D.300, D.302, T.303
- Chain B: P.1, S.4
- Ligands: MG.1, MG.2, EDO.8, ACT.11
18 PLIP interactions:18 interactions with chain A- Hydrogen bonds: A:G.101, A:G.103, A:G.105, A:V.106, A:G.133, A:S.134, A:Y.135, A:G.138, A:T.303, A:T.303
- Water bridges: A:T.62, A:G.103, A:G.103
- Salt bridges: A:H.168, A:H.168
- pi-Stacking: A:F.129, A:F.129, A:Y.135
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Rack, J.G.M. et al., Mechanistic insights into the three steps of poly(ADP-ribosylation) reversal. Nat Commun (2021)
- Release Date
- 2021-06-16
- Peptides
- ADP-ribose glycohydrolase ARH3: A
modified peptide: B - SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
CCCB
DaD
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.86 Å
- Oligo State
- hetero-1-1-mer
- Ligands
- 3 x MG: MAGNESIUM ION(Non-covalent)
- 6 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)
- 8 x ACT: ACETATE ION(Non-functional Binders)
- 1 x AR6: [(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL [HYDROXY-[[(2R,3S,4R,5S)-3,4,5-TRIHYDROXYOXOLAN-2-YL]METHOXY]PHOSPHORYL] HYDROGEN PHOSPHATE(Non-covalent)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Rack, J.G.M. et al., Mechanistic insights into the three steps of poly(ADP-ribosylation) reversal. Nat Commun (2021)
- Release Date
- 2021-06-16
- Peptides
- ADP-ribose glycohydrolase ARH3: A
modified peptide: B - SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
CCCB
DaD