SMTL ID : 6pic.4 (3 other biounits)

Crystal structure of Marinobacter subterrani acetylpolyamine amidohydrolase (msAPAH) complexed with 6-amino-N-hydroxyhexanamide

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.03 Å

Oligo State

homo-dimer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: D.200, H.202, D.289 Ligands: 6XA.5 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.200, A:D.200, A:H.202, A:D.289 ZN.6: 4 residues within 4Å: Chain B: D.200, H.202, D.289 Ligands: 6XA.10 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.200, B:D.200, B:H.202, B:D.289

4 x K: POTASSIUM ION(Non-covalent)

K.2: 6 residues within 4Å: Chain A: D.198, D.200, H.202, S.221, L.222, H.223 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.198, A:D.198, A:D.200, A:H.202, A:S.221 K.3: 5 residues within 4Å: Chain A: F.211, R.214, V.217, T.219, Y.248 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:F.211, A:R.214, A:V.217, A:Y.248, H2O.1 K.7: 6 residues within 4Å: Chain B: D.198, D.200, H.202, S.221, L.222, H.223 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:D.198, B:D.200, B:H.202, B:S.221, B:L.222 K.8: 5 residues within 4Å: Chain B: F.211, R.214, V.217, T.219, Y.248 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:R.214, B:V.217, B:Y.248, H2O.4, H2O.4

2 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 3 residues within 4Å: Chain A: K.88, D.109, D.111 6 PLIP interactions: 2 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:D.109, A:D.111, H2O.1, H2O.2, H2O.3, H2O.3 MG.9: 3 residues within 4Å: Chain B: K.88, D.109, D.111 6 PLIP interactions: 2 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:D.109, B:D.111, H2O.4, H2O.5, H2O.6, H2O.6

2 x 6XA: 6-amino-N-hydroxyhexanamide(Non-covalent)

6XA.5: 13 residues within 4Å: Chain A: E.22, D.122, H.163, H.164, G.172, Y.173, D.200, H.202, F.230, D.289, Y.328 Chain B: F.96 Ligands: ZN.1 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:Y.173, A:F.230 Hydrogen bonds: A:E.22, A:D.122, A:H.164, A:Y.173 Water bridges: A:D.24 6XA.10: 13 residues within 4Å: Chain A: F.96 Chain B: E.22, D.122, H.163, H.164, G.172, Y.173, D.200, H.202, F.230, D.289, Y.328 Ligands: ZN.6 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:F.230 Hydrogen bonds: B:E.22, B:D.122, B:H.164

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Osko, J.D. et al., Structure and Function of the Acetylpolyamine Amidohydrolase from the Deep Earth HalophileMarinobacter subterrani. Biochemistry (2019)

Release Date

2019-09-18

Peptides

Acetylpolyamine Amidohydrolase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
E

B
G

Acetylpolyamine Amidohydrolase

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