- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.42 Å
- Oligo State
- homo-tetramer
- Ligands
- 4 x ZN: ZINC ION(Non-covalent)
- 8 x K: POTASSIUM ION(Non-covalent)
K.2: 7 residues within 4Å:- Chain A: D.180, D.182, H.184, G.186, S.203, L.204, H.205
3 PLIP interactions:3 interactions with chain A- Metal complexes: A:D.182, A:H.184, A:S.203
K.3: 5 residues within 4Å:- Chain A: W.193, D.196, V.199, T.201, Y.228
5 PLIP interactions:3 interactions with chain A, 2 Ligand-Water interactions- Metal complexes: A:D.196, A:V.199, A:Y.228, H2O.12, H2O.12
K.12: 7 residues within 4Å:- Chain B: D.180, D.182, H.184, G.186, S.203, L.204, H.205
3 PLIP interactions:3 interactions with chain B- Metal complexes: B:D.182, B:H.184, B:S.203
K.13: 5 residues within 4Å:- Chain B: W.193, D.196, V.199, T.201, Y.228
5 PLIP interactions:3 interactions with chain B, 2 Ligand-Water interactions- Metal complexes: B:D.196, B:V.199, B:Y.228, H2O.30, H2O.30
K.20: 7 residues within 4Å:- Chain C: D.180, D.182, H.184, G.186, S.203, L.204, H.205
3 PLIP interactions:3 interactions with chain C- Metal complexes: C:D.182, C:H.184, C:S.203
K.21: 5 residues within 4Å:- Chain C: W.193, D.196, V.199, T.201, Y.228
5 PLIP interactions:3 interactions with chain C, 2 Ligand-Water interactions- Metal complexes: C:D.196, C:V.199, C:Y.228, H2O.48, H2O.48
K.30: 7 residues within 4Å:- Chain D: D.180, D.182, H.184, G.186, S.203, L.204, H.205
3 PLIP interactions:3 interactions with chain D- Metal complexes: D:D.182, D:H.184, D:S.203
K.31: 5 residues within 4Å:- Chain D: W.193, D.196, V.199, T.201, Y.228
5 PLIP interactions:3 interactions with chain D, 2 Ligand-Water interactions- Metal complexes: D:D.196, D:V.199, D:Y.228, H2O.66, H2O.66
- 4 x 7H1: 2,2,3,3,4,4,5,5,6,6,7,7-dodecakis(fluoranyl)-~{N}-oxidanyl-~{N}'-phenyl-octanediamide(Non-covalent)
7H1.4: 15 residues within 4Å:- Chain A: L.23, I.102, H.144, H.145, G.153, F.154, D.182, H.184, F.210, D.270, L.277, Y.314
- Chain C: F.343
- Ligands: ZN.1, PEG.28
4 PLIP interactions:4 interactions with chain A- Hydrogen bonds: A:H.145
- Water bridges: A:Y.314, A:Y.314
- Halogen bonds: A:G.153
7H1.14: 15 residues within 4Å:- Chain B: L.23, I.102, H.144, H.145, G.153, F.154, D.182, H.184, F.210, D.270, L.277, Y.314
- Chain D: F.343
- Ligands: ZN.11, PEG.35
3 PLIP interactions:3 interactions with chain B- Hydrogen bonds: B:H.145, B:Y.314
- Halogen bonds: B:G.153
7H1.22: 15 residues within 4Å:- Chain A: F.343
- Chain C: L.23, I.102, H.144, H.145, G.153, F.154, D.182, H.184, F.210, D.270, L.277, Y.314
- Ligands: PEG.10, ZN.19
4 PLIP interactions:4 interactions with chain C- Hydrogen bonds: C:H.145
- Water bridges: C:Y.314, C:Y.314
- Halogen bonds: C:G.153
7H1.32: 15 residues within 4Å:- Chain B: F.343
- Chain D: L.23, I.102, H.144, H.145, G.153, F.154, D.182, H.184, F.210, D.270, L.277, Y.314
- Ligands: PEG.17, ZN.29
3 PLIP interactions:3 interactions with chain D- Hydrogen bonds: D:H.145, D:Y.314
- Halogen bonds: D:G.153
- 4 x 1PE: PENTAETHYLENE GLYCOL(Non-functional Binders)
1PE.5: 6 residues within 4Å:- Chain A: E.174, R.175, P.197, N.224, Y.228, R.371
2 PLIP interactions:2 interactions with chain A- Hydrogen bonds: A:R.175
- Water bridges: A:R.371
1PE.15: 4 residues within 4Å:- Chain B: E.174, R.175, P.197, Y.228
5 PLIP interactions:5 interactions with chain B- Hydrogen bonds: B:R.175
- Water bridges: B:R.175, B:N.224, B:Y.228, B:Y.228
1PE.23: 6 residues within 4Å:- Chain C: E.174, R.175, P.197, N.224, Y.228, R.371
2 PLIP interactions:2 interactions with chain C- Hydrogen bonds: C:R.175
- Water bridges: C:R.371
1PE.33: 4 residues within 4Å:- Chain D: E.174, R.175, P.197, Y.228
5 PLIP interactions:5 interactions with chain D- Hydrogen bonds: D:R.175
- Water bridges: D:R.175, D:N.224, D:Y.228, D:Y.228
- 16 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)
PEG.6: 2 residues within 4Å:- Chain A: H.207
- Chain C: L.353
Ligand excluded by PLIPPEG.7: 3 residues within 4Å:- Chain A: T.94
- Chain D: A.25, M.104
Ligand excluded by PLIPPEG.8: 1 residues within 4Å:- Chain A: R.357
Ligand excluded by PLIPPEG.9: 4 residues within 4Å:- Chain A: Q.190, W.194, D.213, E.219
Ligand excluded by PLIPPEG.10: 6 residues within 4Å:- Chain A: P.339, Y.340
- Chain C: A.24, M.32, I.102
- Ligands: 7H1.22
Ligand excluded by PLIPPEG.16: 3 residues within 4Å:- Chain B: T.94, G.106
- Chain C: A.25
Ligand excluded by PLIPPEG.17: 5 residues within 4Å:- Chain B: P.339, Y.340
- Chain D: M.32, I.102
- Ligands: 7H1.32
Ligand excluded by PLIPPEG.18: 2 residues within 4Å:- Chain B: D.285, H.341
Ligand excluded by PLIPPEG.24: 2 residues within 4Å:- Chain A: L.353
- Chain C: H.207
Ligand excluded by PLIPPEG.25: 3 residues within 4Å:- Chain B: A.25, M.104
- Chain C: T.94
Ligand excluded by PLIPPEG.26: 1 residues within 4Å:- Chain C: R.357
Ligand excluded by PLIPPEG.27: 4 residues within 4Å:- Chain C: Q.190, W.194, D.213, E.219
Ligand excluded by PLIPPEG.28: 6 residues within 4Å:- Chain A: A.24, M.32, I.102
- Chain C: P.339, Y.340
- Ligands: 7H1.4
Ligand excluded by PLIPPEG.34: 3 residues within 4Å:- Chain A: A.25
- Chain D: T.94, G.106
Ligand excluded by PLIPPEG.35: 5 residues within 4Å:- Chain B: M.32, I.102
- Chain D: P.339, Y.340
- Ligands: 7H1.14
Ligand excluded by PLIPPEG.36: 2 residues within 4Å:- Chain D: D.285, H.341
Ligand excluded by PLIP- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Meyners, C. et al., The thermodynamic signature of ligand binding to histone deacetylase-like amidohydrolases is most sensitive to the flexibility in the L2-loop lining the active site pocket. Biochim. Biophys. Acta (2017)
- Release Date
- 2017-04-12
- Peptides
- HISTONE DEACETYLASE-LIKE AMIDOHYDROLASE: ABCD
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
BC
AD
B
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.42 Å
- Oligo State
- homo-tetramer
- Ligands
- 4 x ZN: ZINC ION(Non-covalent)
- 8 x K: POTASSIUM ION(Non-covalent)
- 4 x 7H1: 2,2,3,3,4,4,5,5,6,6,7,7-dodecakis(fluoranyl)-~{N}-oxidanyl-~{N}'-phenyl-octanediamide(Non-covalent)
- 4 x 1PE: PENTAETHYLENE GLYCOL(Non-functional Binders)
- 16 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Meyners, C. et al., The thermodynamic signature of ligand binding to histone deacetylase-like amidohydrolases is most sensitive to the flexibility in the L2-loop lining the active site pocket. Biochim. Biophys. Acta (2017)
- Release Date
- 2017-04-12
- Peptides
- HISTONE DEACETYLASE-LIKE AMIDOHYDROLASE: ABCD
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
BC
AD
B