SMTL ID : 3q9b.6 (5 other biounits)

Crystal Structure of APAH complexed with M344

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.25 Å

Oligo State

homo-dimer

Ligands

18 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.1: 6 residues within 4Å: Chain A: Y.19, G.20 Chain B: W.78, Y.83, E.106 Ligands: B3N.11 Ligand excluded by PLIP DMS.2: 5 residues within 4Å: Chain A: L.60, K.61, V.62, H.63, D.64 Ligand excluded by PLIP DMS.3: 8 residues within 4Å: Chain A: N.114, M.164, N.200, D.204, L.229 Chain B: R.95, R.96, T.97 Ligand excluded by PLIP DMS.4: 2 residues within 4Å: Chain A: I.101, P.102 Ligand excluded by PLIP DMS.5: 6 residues within 4Å: Chain A: I.142, A.186, I.189, E.275, A.276, P.314 Ligand excluded by PLIP DMS.6: 4 residues within 4Å: Chain A: K.61, Q.179, D.183, R.209 Ligand excluded by PLIP DMS.7: 5 residues within 4Å: Chain A: A.232, T.235, A.245, Y.247, R.268 Ligand excluded by PLIP DMS.8: 6 residues within 4Å: Chain A: A.52, R.53, H.54, L.129, M.132, A.133 Ligand excluded by PLIP DMS.9: 6 residues within 4Å: Chain A: W.78, Y.83, E.106 Chain B: Y.19, G.20 Ligands: B3N.24 Ligand excluded by PLIP DMS.10: 8 residues within 4Å: Chain A: R.95, R.96, T.97 Chain B: N.114, M.164, N.200, D.204, L.229 Ligand excluded by PLIP DMS.16: 6 residues within 4Å: Chain A: Y.207, L.229, E.234 Chain B: R.96, T.97, S.98 Ligand excluded by PLIP DMS.17: 4 residues within 4Å: Chain B: L.60, K.61, H.63, D.64 Ligand excluded by PLIP DMS.18: 3 residues within 4Å: Chain B: I.101, P.102, T.103 Ligand excluded by PLIP DMS.19: 5 residues within 4Å: Chain B: I.142, A.186, I.189, E.275, A.276 Ligand excluded by PLIP DMS.20: 3 residues within 4Å: Chain B: Q.179, D.183, R.209 Ligand excluded by PLIP DMS.21: 4 residues within 4Å: Chain B: A.232, N.246, Y.247, R.268 Ligand excluded by PLIP DMS.22: 5 residues within 4Å: Chain A: R.96, T.97, S.98 Chain B: Y.207, E.234 Ligand excluded by PLIP DMS.23: 4 residues within 4Å: Chain B: R.53, H.54, L.129, A.133 Ligand excluded by PLIP

2 x B3N: 4-(dimethylamino)-N-[7-(hydroxyamino)-7-oxoheptyl]benzamide(Non-covalent)

B3N.11: 16 residues within 4Å: Chain A: Y.19, F.27, E.117, H.158, H.159, G.167, Y.168, D.195, H.197, F.225, D.284, P.290, I.291, G.321 Ligands: DMS.1, ZN.14 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:Y.19, A:F.27, A:E.117, A:Y.168, A:F.225, A:I.291 Hydrogen bonds: A:H.159, A:Y.168, A:H.197 Water bridges: A:F.225 B3N.24: 16 residues within 4Å: Chain B: Y.19, F.27, E.117, H.158, H.159, G.167, Y.168, D.195, H.197, F.225, D.284, P.290, I.291, G.321 Ligands: DMS.9, ZN.27 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:Y.19, B:F.27, B:E.117, B:Y.168, B:F.225, B:I.291 Hydrogen bonds: B:H.159, B:G.322 Water bridges: B:E.17, B:Y.168, B:F.225

4 x K: POTASSIUM ION(Non-covalent)

K.12: 6 residues within 4Å: Chain A: D.193, D.195, H.197, S.216, L.217, H.218 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.193, A:D.195, A:H.197, A:S.216, A:L.217 K.15: 6 residues within 4Å: Chain A: F.286, E.287, D.289, S.292, F.293, F.294 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.289, A:S.292, H2O.6 K.25: 6 residues within 4Å: Chain B: D.193, D.195, H.197, S.216, L.217, H.218 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:D.193, B:D.193, B:D.195, B:H.197, B:S.216 K.28: 5 residues within 4Å: Chain B: F.286, E.287, D.289, S.292, F.294 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:F.286, B:D.289, B:S.292, B:S.292, H2O.13

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

NA.13: 4 residues within 4Å: Chain A: F.206, R.209, V.212, T.243 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:F.206, A:R.209, A:T.243 Water bridges: A:T.244 NA.26: 4 residues within 4Å: Chain B: F.206, R.209, V.212, T.243 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.209, B:T.243, B:T.243 Water bridges: B:T.244

2 x ZN: ZINC ION(Non-covalent)

ZN.14: 4 residues within 4Å: Chain A: D.195, H.197, D.284 Ligands: B3N.11 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.195, A:D.195, A:H.197, A:D.284 ZN.27: 4 residues within 4Å: Chain B: D.195, H.197, D.284 Ligands: B3N.24 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.195, B:D.195, B:H.197, B:D.284

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lombardi, P.M. et al., Structure of prokaryotic polyamine deacetylase reveals evolutionary functional relationships with eukaryotic histone deacetylases . Biochemistry (2011)

Release Date

2011-03-02

Peptides

Acetylpolyamine amidohydrolase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
G

B
L

Acetylpolyamine amidohydrolase

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