SMTL ID : 2z5x.2 (1 other biounit)

Crystal Structure of Human Monoamine Oxidase A with Harmine

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-tetramer

Ligands

4 x FAD: FLAVIN-ADENINE DINUCLEOTIDE(Covalent)

FAD.1: 37 residues within 4Å: Chain A: I.8, G.9, G.10, G.11, I.12, S.13, L.31, E.32, A.33, R.34, G.38, G.39, R.40, T.41, V.54, G.55, G.56, A.57, Y.58, H.231, P.232, V.233, A.261, I.262, L.266, V.292, W.386, Y.391, C.395, Y.396, G.423, T.424, G.432, Y.433, M.434, A.437 Ligands: HRM.2 33 PLIP interactions: 33 interactions with chain A Hydrophobic interactions: A:R.40, A:V.292, A:W.386, A:Y.396 Hydrogen bonds: A:G.10, A:G.10, A:S.13, A:A.33, A:R.34, A:R.34, A:G.38, A:R.40, A:G.56, A:A.57, A:Y.58, A:Y.58, A:V.233, A:V.233, A:T.424, A:G.432, A:M.434 Water bridges: A:G.11, A:I.12, A:I.12, A:G.14, A:G.39, A:R.40, A:R.40, A:Q.63, A:E.435 Salt bridges: A:R.40, A:R.40 pi-Stacking: A:Y.391 FAD.8: 37 residues within 4Å: Chain B: I.8, G.9, G.10, G.11, I.12, S.13, L.31, E.32, A.33, R.34, G.38, G.39, R.40, T.41, V.54, G.55, G.56, A.57, Y.58, H.231, P.232, V.233, A.261, I.262, L.266, V.292, W.386, Y.391, C.395, Y.396, G.423, T.424, G.432, Y.433, M.434, A.437 Ligands: HRM.9 33 PLIP interactions: 33 interactions with chain B Hydrophobic interactions: B:R.40, B:V.292, B:W.386, B:Y.396 Hydrogen bonds: B:G.10, B:G.10, B:S.13, B:A.33, B:R.34, B:R.34, B:G.38, B:R.40, B:G.56, B:A.57, B:Y.58, B:Y.58, B:V.233, B:V.233, B:T.424, B:G.432, B:M.434 Water bridges: B:G.11, B:I.12, B:I.12, B:G.14, B:G.39, B:R.40, B:R.40, B:Q.63, B:E.435 Salt bridges: B:R.40, B:R.40 pi-Stacking: B:Y.391 FAD.15: 37 residues within 4Å: Chain C: I.8, G.9, G.10, G.11, I.12, S.13, L.31, E.32, A.33, R.34, G.38, G.39, R.40, T.41, V.54, G.55, G.56, A.57, Y.58, H.231, P.232, V.233, A.261, I.262, L.266, V.292, W.386, Y.391, C.395, Y.396, G.423, T.424, G.432, Y.433, M.434, A.437 Ligands: HRM.16 34 PLIP interactions: 34 interactions with chain C Hydrophobic interactions: C:R.40, C:V.292, C:W.386, C:Y.396 Hydrogen bonds: C:G.10, C:G.10, C:S.13, C:A.33, C:R.34, C:R.34, C:G.38, C:R.40, C:G.56, C:A.57, C:Y.58, C:Y.58, C:V.233, C:V.233, C:T.424, C:T.424, C:G.432, C:M.434 Water bridges: C:G.11, C:I.12, C:I.12, C:G.14, C:G.39, C:R.40, C:R.40, C:Q.63, C:E.435 Salt bridges: C:R.40, C:R.40 pi-Stacking: C:Y.391 FAD.22: 37 residues within 4Å: Chain D: I.8, G.9, G.10, G.11, I.12, S.13, L.31, E.32, A.33, R.34, G.38, G.39, R.40, T.41, V.54, G.55, G.56, A.57, Y.58, H.231, P.232, V.233, A.261, I.262, L.266, V.292, W.386, Y.391, C.395, Y.396, G.423, T.424, G.432, Y.433, M.434, A.437 Ligands: HRM.23 34 PLIP interactions: 34 interactions with chain D Hydrophobic interactions: D:R.40, D:V.292, D:W.386, D:Y.396 Hydrogen bonds: D:G.10, D:G.10, D:S.13, D:A.33, D:R.34, D:R.34, D:G.38, D:R.40, D:G.56, D:A.57, D:Y.58, D:Y.58, D:V.233, D:V.233, D:T.424, D:T.424, D:G.432, D:M.434 Water bridges: D:G.11, D:I.12, D:I.12, D:G.14, D:G.39, D:R.40, D:R.40, D:Q.63, D:E.435 Salt bridges: D:R.40, D:R.40 pi-Stacking: D:Y.391

4 x HRM: 7-METHOXY-1-METHYL-9H-BETA-CARBOLINE(Non-covalent)

HRM.2: 12 residues within 4Å: Chain A: Y.58, I.169, N.170, F.197, Q.204, C.312, I.324, L.326, F.341, Y.396, Y.433 Ligands: FAD.1 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:Y.58, A:I.169, A:Q.204, A:I.324, A:I.324, A:L.326, A:L.326, A:F.341, A:Y.396 Water bridges: A:Q.204 HRM.9: 12 residues within 4Å: Chain B: Y.58, I.169, N.170, F.197, Q.204, C.312, I.324, L.326, F.341, Y.396, Y.433 Ligands: FAD.8 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:Y.58, B:I.169, B:Q.204, B:I.324, B:I.324, B:L.326, B:L.326, B:F.341, B:Y.396 Water bridges: B:Q.204 HRM.16: 12 residues within 4Å: Chain C: Y.58, I.169, N.170, F.197, Q.204, C.312, I.324, L.326, F.341, Y.396, Y.433 Ligands: FAD.15 10 PLIP interactions: 10 interactions with chain C Hydrophobic interactions: C:Y.58, C:I.169, C:Q.204, C:I.324, C:I.324, C:L.326, C:L.326, C:F.341, C:Y.396 Water bridges: C:Q.204 HRM.23: 12 residues within 4Å: Chain D: Y.58, I.169, N.170, F.197, Q.204, C.312, I.324, L.326, F.341, Y.396, Y.433 Ligands: FAD.22 10 PLIP interactions: 10 interactions with chain D Hydrophobic interactions: D:Y.58, D:I.169, D:Q.204, D:I.324, D:I.324, D:L.326, D:L.326, D:F.341, D:Y.396 Water bridges: D:Q.204

8 x DCX: DECYL(DIMETHYL)PHOSPHINE OXIDE(Non-covalent)

DCX.3: 6 residues within 4Å: Chain A: V.104, W.105, P.107, Y.110, L.111 Chain D: T.498 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain D Hydrophobic interactions: A:W.105, A:P.107, A:Y.110, A:L.111, D:T.498 DCX.4: 4 residues within 4Å: Chain A: Y.110, T.478, W.480 Ligands: DCX.18 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:W.480 Hydrogen bonds: A:E.481 DCX.10: 6 residues within 4Å: Chain B: V.104, W.105, P.107, Y.110, L.111 Chain C: T.498 5 PLIP interactions: 1 interactions with chain C, 4 interactions with chain B Hydrophobic interactions: C:T.498, B:W.105, B:P.107, B:Y.110, B:L.111 DCX.11: 4 residues within 4Å: Chain B: Y.110, T.478, W.480 Ligands: DCX.25 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:W.480 Hydrogen bonds: B:E.481 DCX.17: 6 residues within 4Å: Chain B: T.498 Chain C: V.104, W.105, P.107, Y.110, L.111 5 PLIP interactions: 4 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: C:W.105, C:P.107, C:Y.110, C:L.111, B:T.498 DCX.18: 4 residues within 4Å: Chain C: Y.110, T.478, W.480 Ligands: DCX.4 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:W.480 Hydrogen bonds: C:T.478, C:E.481 DCX.24: 6 residues within 4Å: Chain A: T.498 Chain D: V.104, W.105, P.107, Y.110, L.111 5 PLIP interactions: 4 interactions with chain D, 1 interactions with chain A Hydrophobic interactions: D:W.105, D:P.107, D:Y.110, D:L.111, A:T.498 DCX.25: 4 residues within 4Å: Chain D: Y.110, T.478, W.480 Ligands: DCX.11 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:W.480 Hydrogen bonds: D:T.478, D:E.481

12 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 6 residues within 4Å: Chain A: R.34, D.35, R.36, Y.42, K.384, E.389 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.34, A:D.35, A:R.36, A:K.384, A:K.384 Water bridges: A:D.35 GOL.6: 9 residues within 4Å: Chain A: Y.51, V.52, D.53, Y.78, K.207, F.208, G.211, D.328, K.330 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:D.53, A:D.53, A:K.207, A:D.328, A:D.328 Water bridges: A:D.53, A:F.208, A:D.328, A:K.330 GOL.7: 7 residues within 4Å: Chain A: N.64, L.67, R.68, K.71, P.465, S.467, D.469 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:N.64, A:R.68, A:D.469, A:D.469, A:D.469 Water bridges: A:N.64, A:K.71 GOL.12: 6 residues within 4Å: Chain B: R.34, D.35, R.36, Y.42, K.384, E.389 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:R.34, B:D.35, B:R.36, B:K.384, B:K.384 Water bridges: B:D.35 GOL.13: 9 residues within 4Å: Chain B: Y.51, V.52, D.53, Y.78, K.207, F.208, G.211, D.328, K.330 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:D.53, B:D.53, B:K.207, B:D.328, B:D.328 Water bridges: B:D.53, B:F.208, B:D.328, B:K.330 GOL.14: 7 residues within 4Å: Chain B: N.64, L.67, R.68, K.71, P.465, S.467, D.469 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:N.64, B:R.68, B:D.469, B:D.469, B:D.469 Water bridges: B:N.64, B:K.71 GOL.19: 6 residues within 4Å: Chain C: R.34, D.35, R.36, Y.42, K.384, E.389 8 PLIP interactions: 8 interactions with chain C Hydrogen bonds: C:R.34, C:D.35, C:R.36, C:K.384, C:K.384 Water bridges: C:D.35, C:Y.42, C:E.389 GOL.20: 9 residues within 4Å: Chain C: Y.51, V.52, D.53, Y.78, K.207, F.208, G.211, D.328, K.330 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:D.53, C:K.207, C:D.328, C:D.328 Water bridges: C:D.53, C:F.208, C:K.330 GOL.21: 7 residues within 4Å: Chain C: N.64, L.67, R.68, K.71, P.465, S.467, D.469 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:N.64, C:R.68, C:D.469, C:D.469 Water bridges: C:N.64, C:K.71 GOL.26: 6 residues within 4Å: Chain D: R.34, D.35, R.36, Y.42, K.384, E.389 8 PLIP interactions: 8 interactions with chain D Hydrogen bonds: D:R.34, D:D.35, D:R.36, D:K.384, D:K.384 Water bridges: D:D.35, D:Y.42, D:E.389 GOL.27: 9 residues within 4Å: Chain D: Y.51, V.52, D.53, Y.78, K.207, F.208, G.211, D.328, K.330 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:D.53, D:K.207, D:D.328, D:D.328 Water bridges: D:D.53, D:F.208, D:K.330 GOL.28: 7 residues within 4Å: Chain D: N.64, L.67, R.68, K.71, P.465, S.467, D.469 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:N.64, D:R.68, D:D.469, D:D.469 Water bridges: D:N.64, D:K.71

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Son, S.Y. et al., Structure of human monoamine oxidase A at 2.2-A resolution: The control of opening the entry for substrates/inhibitors. Proc.Natl.Acad.Sci.Usa (2008)

Release Date

2008-04-01

Peptides

Amine oxidase [flavin-containing] A: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

Amine oxidase [flavin-containing] A

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