SMTL ID : 7d9j.1 (1 other biounit)

SpdH Spermidine dehydrogenase Y443A mutant

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.19 Å

Oligo State

monomer

Ligands

1 x FAD: FLAVIN-ADENINE DINUCLEOTIDE(Non-covalent)

FAD.1: 37 residues within 4Å: Chain A: V.79, G.80, G.82, I.83, S.84, I.104, E.105, N.106, H.107, G.111, G.112, H.113, G.131, S.132, E.133, S.134, Y.324, N.332, S.379, T.380, A.381, A.412, C.413, Y.414, M.417, L.421, W.560, G.563, Y.564, N.596, S.597, A.603, Y.604, A.605, A.608 Ligands: HEM.2, GOL.3 33 PLIP interactions: 33 interactions with chain A Hydrophobic interactions: A:Y.564 Hydrogen bonds: A:G.82, A:I.83, A:S.84, A:N.106, A:N.106, A:H.113, A:H.113, A:S.132, A:S.132, A:E.133, A:S.134, A:S.134, A:Y.324, A:N.332, A:A.381, A:A.381, A:Y.414, A:N.596, A:S.597, A:A.605 Water bridges: A:G.85, A:E.105, A:H.113, A:A.114, A:A.114, A:K.115, A:Q.136, A:Y.414, A:K.438 Salt bridges: A:H.113 pi-Stacking: A:Y.414, A:Y.564

1 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Non-covalent)

HEM.2: 18 residues within 4Å: Chain A: S.45, F.50, A.53, H.54, W.58, N.106, Y.414, M.416, M.417, Y.420, R.515, R.518, S.519, Y.522, R.559, S.561, H.562 Ligands: FAD.1 20 PLIP interactions: 20 interactions with chain A, Hydrophobic interactions: A:F.50, A:F.50, A:F.50, A:A.53, A:W.58, A:Y.414, A:R.518, A:R.518, A:Y.522 Hydrogen bonds: A:Y.420 Water bridges: A:S.434, A:R.518, A:R.518 Salt bridges: A:R.518, A:H.562 pi-Stacking: A:W.58, A:W.58 pi-Cation interactions: A:R.518 Metal complexes: A:H.54, A:H.562

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 6 residues within 4Å: Chain A: E.133, D.282, F.283, Y.324, Y.564 Ligands: FAD.1 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.133, A:D.282, A:Y.564

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Che, S. et al., Structure of Pseudomonas aeruginosa spermidine dehydrogenase: a polyamine oxidase with a novel heme-binding fold. Febs J. (2022)

Release Date

2021-11-17

Peptides

Spermidine dehydrogenase, SpdH: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Spermidine dehydrogenase, SpdH

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