SMTL ID : 6yt2.1

Crystal Structure of human monoamine oxidase B in complex with Diphenylene iodonium (DPI)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-dimer

Ligands

2 x FAD: FLAVIN-ADENINE DINUCLEOTIDE(Non-covalent)(Covalent)

FAD.1: 38 residues within 4Å: Chain A: V.9, G.10, G.11, G.12, I.13, S.14, L.32, E.33, A.34, R.35, G.39, G.40, R.41, T.42, L.55, G.56, G.57, S.58, Y.59, R.232, P.233, V.234, A.262, I.263, P.264, L.267, V.293, W.387, Y.392, C.396, Y.397, G.424, T.425, G.433, Y.434, M.435, A.438 Ligands: PJW.2 32 PLIP interactions: 32 interactions with chain A Hydrophobic interactions: A:V.293, A:W.387, A:Y.397, A:Y.397 Hydrogen bonds: A:G.11, A:G.12, A:S.14, A:A.34, A:R.35, A:R.41, A:G.57, A:S.58, A:Y.59, A:Y.59, A:V.234, A:V.234, A:T.425, A:T.425, A:G.433, A:M.435 Water bridges: A:I.13, A:G.15, A:E.33, A:E.33, A:R.41, A:R.41, A:T.42, A:Q.64, A:E.436 Salt bridges: A:R.41, A:R.41 pi-Stacking: A:Y.392 FAD.5: 36 residues within 4Å: Chain B: V.9, G.10, G.11, G.12, I.13, S.14, L.32, E.33, A.34, R.35, G.39, G.40, R.41, T.42, G.56, G.57, S.58, Y.59, R.232, P.233, V.234, A.262, I.263, P.264, V.293, W.387, Y.392, C.396, Y.397, G.424, T.425, G.433, Y.434, M.435, A.438 Ligands: PJW.6 30 PLIP interactions: 30 interactions with chain B Hydrophobic interactions: B:V.293, B:W.387, B:Y.397 Hydrogen bonds: B:G.11, B:G.12, B:S.14, B:A.34, B:R.35, B:R.41, B:G.57, B:S.58, B:Y.59, B:Y.59, B:V.234, B:V.234, B:T.425, B:G.433, B:M.435 Water bridges: B:I.13, B:G.15, B:E.33, B:E.33, B:R.41, B:R.41, B:T.42, B:Q.64, B:E.436 Salt bridges: B:R.41, B:R.41 pi-Stacking: B:Y.392

2 x PJW: benzo[b][1]benziodole(Non-covalent)

PJW.2: 12 residues within 4Å: Chain A: Y.59, L.170, C.171, I.197, I.198, Q.205, Y.325, L.327, F.342, Y.397, Y.434 Ligands: FAD.1 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:Y.59, A:L.170, A:L.170, A:L.170, A:I.198, A:Q.205, A:Y.325, A:L.327, A:F.342 PJW.6: 12 residues within 4Å: Chain B: Y.59, L.170, C.171, I.197, I.198, Q.205, Y.325, L.327, F.342, Y.397, Y.434 Ligands: FAD.5 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:Y.59, B:Y.59, B:L.170, B:L.170, B:I.198, B:Q.205, B:Y.325, B:L.327, B:F.342

2 x C15: N-DODECYL-N,N-DIMETHYL-3-AMMONIO-1-PROPANESULFONATE(Non-covalent)

C15.3: 4 residues within 4Å: Chain A: D.152, K.153, C.155, W.156 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:W.156, A:W.156 pi-Cation interactions: A:W.156, A:W.156 C15.7: 4 residues within 4Å: Chain B: D.152, K.153, C.155, W.156 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:W.156 pi-Cation interactions: B:W.156, B:W.156

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 6 residues within 4Å: Chain A: H.90, G.93, D.317, A.321, L.366, K.369 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.317, A:K.369, A:K.369 Water bridges: A:G.93 GOL.8: 6 residues within 4Å: Chain B: H.90, G.93, E.320, A.321, L.366, K.369 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:G.93 Water bridges: B:G.93

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Iacovino, L.G. et al., Diphenylene Iodonium Is a Noncovalent MAO Inhibitor: A Biochemical and Structural Analysis. Chemmedchem (2020)

Release Date

2020-06-10

Peptides

Amine oxidase [flavin-containing] B: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Amine oxidase [flavin-containing] B

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