- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.05 Å
- Oligo State
- monomer
- Ligands
- 7 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)
- 1 x X51: 1-[(4-aminobutyl)amino]ethane-1,1-diol(Non-covalent)
X51.2: 14 residues within 4Å:- Chain A: E.26, A.96, P.136, H.138, G.147, F.148, D.176, H.178, W.207, D.269, E.276, G.307, Y.309
- Ligands: ZN.11
8 PLIP interactions:8 interactions with chain A- Hydrophobic interactions: A:P.136, A:F.148, A:F.148, A:W.207
- Hydrogen bonds: A:E.26, A:Y.309
- Salt bridges: A:H.138, A:H.178
- 2 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)
PEG.3: 7 residues within 4Å:- Chain A: S.5, G.6, S.7, R.127, L.325, L.326
- Ligands: EDO.6
2 PLIP interactions:2 interactions with chain A- Hydrogen bonds: A:G.6, A:S.7
PEG.4: 7 residues within 4Å:- Chain A: A.4, V.121, R.124, V.126, R.127, A.298, K.300
3 PLIP interactions:3 interactions with chain A- Hydrogen bonds: A:V.121, A:R.124, A:R.124
- 1 x ZN: ZINC ION(Non-covalent)
- 2 x K: POTASSIUM ION(Non-covalent)
K.12: 5 residues within 4Å:- Chain A: D.174, D.176, H.178, S.197, W.198
5 PLIP interactions:5 interactions with chain A- Metal complexes: A:D.174, A:D.174, A:D.176, A:H.178, A:S.197
K.13: 4 residues within 4Å:- Chain A: F.187, D.190, V.193, F.226
5 PLIP interactions:3 interactions with chain A, 2 Ligand-Water interactions- Metal complexes: A:F.187, A:D.190, A:V.193, H2O.2, H2O.9
- 4 x PO4: PHOSPHATE ION(Non-functional Binders)
PO4.14: 2 residues within 4Å:- Chain A: Q.58, K.108
4 PLIP interactions:4 interactions with chain A- Hydrogen bonds: A:Q.58
- Water bridges: A:K.108, A:K.108
- Salt bridges: A:K.108
PO4.15: 5 residues within 4Å:- Chain A: H.203, N.233, K.234, S.342, E.345
6 PLIP interactions:6 interactions with chain A- Hydrogen bonds: A:S.342
- Water bridges: A:N.233, A:K.234, A:K.234
- Salt bridges: A:H.203, A:K.234
PO4.16: 5 residues within 4Å:- Chain A: H.45, H.323, K.409, R.410, M.411
3 PLIP interactions:3 interactions with chain A- Hydrogen bonds: A:R.410
- Salt bridges: A:H.45, A:H.323
PO4.17: 6 residues within 4Å:- Chain A: V.54, Q.116, D.119, S.120, K.123, E.125
5 PLIP interactions:5 interactions with chain A- Hydrogen bonds: A:Q.116, A:D.119, A:E.125
- Water bridges: A:Q.116
- Salt bridges: A:K.123
- 1 x NA: SODIUM ION(Non-functional Binders)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Herbst-Gervasoni, C.J. et al., X-ray Crystallographic Snapshots of Substrate Binding in the Active Site of Histone Deacetylase 10. Biochemistry (2021)
- Release Date
- 2021-02-03
- Peptides
- Polyamine deacetylase HDAC10: A
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
A
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.05 Å
- Oligo State
- monomer
- Ligands
- 7 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)
- 1 x X51: 1-[(4-aminobutyl)amino]ethane-1,1-diol(Non-covalent)
- 2 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)
- 1 x ZN: ZINC ION(Non-covalent)
- 2 x K: POTASSIUM ION(Non-covalent)
- 4 x PO4: PHOSPHATE ION(Non-functional Binders)
- 1 x NA: SODIUM ION(Non-functional Binders)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Herbst-Gervasoni, C.J. et al., X-ray Crystallographic Snapshots of Substrate Binding in the Active Site of Histone Deacetylase 10. Biochemistry (2021)
- Release Date
- 2021-02-03
- Peptides
- Polyamine deacetylase HDAC10: A
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
A