- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.36 Å
- Oligo State
- homo-dimer
- Ligands
- 2 x SEF: ethyl (R)-{10-[(hept-6-yn-1-ylcarbamoyl)oxy]decyl}phosphonofluoridate(Covalent)
- 2 x CL: CHLORIDE ION(Non-functional Binders)
- 10 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)
EDO.3: 5 residues within 4Å:- Chain A: D.10, G.32, V.33, A.36
- Ligands: EDO.7
No protein-ligand interaction detected (PLIP)EDO.4: 8 residues within 4Å:- Chain A: V.33, T.111, S.112, W.113, G.114, A.115
- Ligands: CL.2, EDO.7
3 PLIP interactions:3 interactions with chain A- Hydrogen bonds: A:W.113, A:A.115
- Water bridges: A:S.112
EDO.5: 6 residues within 4Å:- Chain A: G.41, G.42, P.43, S.44, G.66, N.67
5 PLIP interactions:5 interactions with chain A- Hydrogen bonds: A:G.42, A:S.44, A:S.44
- Water bridges: A:G.66, A:N.67
EDO.6: 6 residues within 4Å:- Chain A: S.112, G.114, V.117, A.122, H.126, Y.155
3 PLIP interactions:3 interactions with chain A- Hydrogen bonds: A:S.112, A:Y.155
- Water bridges: A:S.112
EDO.7: 10 residues within 4Å:- Chain A: G.9, D.10, I.11, V.33, T.111, V.145, H.146, G.147
- Ligands: EDO.3, EDO.4
3 PLIP interactions:3 interactions with chain A- Hydrogen bonds: A:D.10, A:I.11, A:H.146
EDO.13: 5 residues within 4Å:- Chain B: D.10, G.32, V.33, A.36
- Ligands: EDO.17
No protein-ligand interaction detected (PLIP)EDO.14: 8 residues within 4Å:- Chain B: V.33, T.111, S.112, W.113, G.114, A.115
- Ligands: CL.12, EDO.17
4 PLIP interactions:4 interactions with chain B- Hydrogen bonds: B:T.111, B:W.113, B:A.115
- Water bridges: B:S.112
EDO.15: 6 residues within 4Å:- Chain B: G.41, G.42, P.43, S.44, G.66, N.67
5 PLIP interactions:5 interactions with chain B- Hydrogen bonds: B:G.42, B:S.44, B:S.44
- Water bridges: B:G.66, B:N.67
EDO.16: 6 residues within 4Å:- Chain B: S.112, G.114, V.117, A.122, H.126, Y.155
3 PLIP interactions:3 interactions with chain B- Hydrogen bonds: B:S.112
- Water bridges: B:S.112, B:Y.155
EDO.17: 10 residues within 4Å:- Chain B: G.9, D.10, I.11, V.33, T.111, V.145, H.146, G.147
- Ligands: EDO.13, EDO.14
4 PLIP interactions:4 interactions with chain B- Hydrogen bonds: B:D.10, B:D.10, B:I.11, B:H.146
- 2 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)
PEG.8: 6 residues within 4Å:- Chain A: G.9, D.10, I.11, E.13, F.14, V.145
3 PLIP interactions:3 interactions with chain A- Hydrogen bonds: A:D.10
- Water bridges: A:Q.8, A:Q.8
PEG.18: 6 residues within 4Å:- Chain B: G.9, D.10, I.11, E.13, F.14, V.145
3 PLIP interactions:3 interactions with chain B- Hydrogen bonds: B:D.10
- Water bridges: B:Q.8, B:Q.8
- 4 x GOL: GLYCEROL(Non-functional Binders)
GOL.9: 0 residues within 4Å:- (No contacts)
No protein-ligand interaction detected (PLIP)GOL.10: 8 residues within 4Å:- Chain A: G.80, D.81, E.82, P.83
- Chain B: L.38, P.43, Q.46, E.47
5 PLIP interactions:1 interactions with chain B, 4 interactions with chain A- Water bridges: B:P.43, A:Y.26, A:G.80, A:G.80
- Hydrogen bonds: A:Y.26
GOL.19: 0 residues within 4Å:- (No contacts)
No protein-ligand interaction detected (PLIP)GOL.20: 8 residues within 4Å:- Chain A: L.38, P.43, Q.46, E.47
- Chain B: G.80, D.81, E.82, P.83
5 PLIP interactions:4 interactions with chain B, 1 interactions with chain A- Hydrogen bonds: B:Y.26, B:Y.26
- Water bridges: B:G.80, B:G.80, A:P.43
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Rajagopalan, S. et al., Design of activated serine-containing catalytic triads with atomic-level accuracy. Nat.Chem.Biol. (2014)
- Release Date
- 2013-04-10
- Peptides
- Evolved variant of computationally designed serine hydrolase OSH55.4_H1: AB
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
A
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.36 Å
- Oligo State
- homo-dimer
- Ligands
- 2 x SEF: ethyl (R)-{10-[(hept-6-yn-1-ylcarbamoyl)oxy]decyl}phosphonofluoridate(Covalent)
- 2 x CL: CHLORIDE ION(Non-functional Binders)
- 10 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)
- 2 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)
- 4 x GOL: GLYCEROL(Non-functional Binders)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Rajagopalan, S. et al., Design of activated serine-containing catalytic triads with atomic-level accuracy. Nat.Chem.Biol. (2014)
- Release Date
- 2013-04-10
- Peptides
- Evolved variant of computationally designed serine hydrolase OSH55.4_H1: AB
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
A