SMTL ID : 7oxl.1

Crystal structure of human Spermine Oxidase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-dimer

Ligands

2 x 6YU: FAD-MDL72527 adduct(Non-covalent)

6YU.1: 38 residues within 4Å: Chain A: I.10, G.11, A.12, G.13, L.14, A.15, L.34, E.35, A.36, G.41, G.42, R.43, V.44, L.56, G.57, A.58, T.59, W.60, E.188, S.190, P.240, V.241, T.275, V.276, F.288, T.309, W.371, W.416, Y.421, F.422, S.425, Y.426, G.454, E.455, S.463, T.464, T.465, A.468 30 PLIP interactions: 30 interactions with chain A Hydrophobic interactions: A:R.43, A:W.60, A:W.371, A:W.416, A:Y.426 Hydrogen bonds: A:A.12, A:G.13, A:A.15, A:A.36, A:G.41, A:R.43, A:T.59, A:W.60, A:W.60, A:V.241, A:V.241, A:E.455, A:T.465 Water bridges: A:L.14, A:L.14, A:G.16, A:S.37, A:G.42, A:R.43, A:R.43, A:S.277 Salt bridges: A:R.43, A:R.43 pi-Stacking: A:Y.421, A:Y.426 6YU.5: 38 residues within 4Å: Chain B: I.10, G.11, A.12, G.13, L.14, A.15, L.34, E.35, A.36, G.41, G.42, R.43, V.44, L.56, G.57, A.58, T.59, W.60, E.188, S.190, P.240, V.241, T.275, V.276, F.288, T.309, W.371, W.416, Y.421, F.422, S.425, Y.426, G.454, E.455, S.463, T.464, T.465, A.468 30 PLIP interactions: 30 interactions with chain B Hydrophobic interactions: B:R.43, B:W.60, B:W.371, B:W.416, B:Y.426 Hydrogen bonds: B:A.12, B:G.13, B:A.15, B:A.36, B:G.41, B:R.43, B:T.59, B:W.60, B:W.60, B:V.241, B:V.241, B:E.455, B:T.465 Water bridges: B:L.14, B:L.14, B:G.16, B:S.37, B:G.42, B:R.43, B:R.43, B:S.277 Salt bridges: B:R.43, B:R.43 pi-Stacking: B:Y.421, B:Y.426

4 x CL: CHLORIDE ION(Non-functional Binders)

CL.2: 2 residues within 4Å: Chain A: H.245, R.290 Ligand excluded by PLIP CL.4: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.6: 2 residues within 4Å: Chain B: H.245, R.290 Ligand excluded by PLIP CL.8: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP

2 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.3: 9 residues within 4Å: Chain A: T.53, E.55, T.59, W.60, K.311, F.313, L.358, Y.364, S.369 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:T.59, A:W.60, A:F.313, A:L.358, A:Y.364 Hydrogen bonds: A:E.55, A:E.55, A:K.311, A:S.369 MPD.7: 9 residues within 4Å: Chain B: T.53, E.55, T.59, W.60, K.311, F.313, L.358, Y.364, S.369 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:T.59, B:W.60, B:F.313, B:L.358, B:Y.364 Hydrogen bonds: B:E.55, B:E.55, B:K.311, B:S.369

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Diaz, E. et al., Structure of human spermine oxidase in complex with a highly selective allosteric inhibitor. Commun Biol (2022)

Release Date

2022-07-13

Peptides

Spermine oxidase,Spermine oxidase,Spermine oxidase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Spermine oxidase,Spermine oxidase,Spermine oxidase

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