SMTL ID : 6pia.2 (1 other biounit)

Crystal structure of Marinobacter subterrani acetylpolyamine amidohydrolase (msAPAH) complexed with 6-[(3-aminopropyl)amino]-N-hydroxyhexanamide

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.75 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: XS6.5 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: XS6.11 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: 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.5 K.3: 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.7: 5 residues within 4Å: Chain B: F.211, R.214, V.217, T.219, Y.248 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:F.211, B:R.214, B:V.217, B:Y.248, H2O.10 K.8: 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.198, B:D.200, B:H.202, B:S.221

2 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 2 residues within 4Å: Chain A: 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.4, H2O.4, H2O.9, H2O.9 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.1, H2O.4, H2O.8, H2O.12

2 x XS6: 6-[(3-aminopropyl)amino]-N-hydroxyhexanamide(Non-covalent)

XS6.5: 18 residues within 4Å: Chain A: E.22, L.23, D.24, D.122, H.163, H.164, G.172, Y.173, D.200, H.202, F.230, D.289, I.296, G.326, Y.328 Chain B: T.95, F.96 Ligands: ZN.1 9 PLIP interactions: 8 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:D.122, A:Y.173, A:F.230, A:F.230, B:F.96 Hydrogen bonds: A:L.23, A:D.24, A:H.164, A:Y.328 XS6.11: 18 residues within 4Å: Chain A: T.95, F.96 Chain B: E.22, L.23, D.24, D.122, H.163, H.164, G.172, Y.173, D.200, H.202, F.230, D.289, I.296, G.326, Y.328 Ligands: ZN.6 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:Y.173, B:F.230, B:F.230 Hydrogen bonds: B:E.22, B:E.22, B:D.24, B:D.122, B:H.164

1 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.10: 7 residues within 4Å: Chain B: L.13, P.56, E.57, E.58, R.134, A.135, N.138 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.134, B:N.138

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
D

B
C

Acetylpolyamine amidohydrolase

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