SMTL ID : 6m0p.1

Hydroxylamine oxidoreductase in complex with juglone

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.78 Å

Oligo State

hetero-3-3-mer

Ligands

21 x HEC: HEME C(Covalent)

HEC.1: 23 residues within 4Å: Chain A: Y.140, K.141, K.144, C.196, H.200, E.203, F.204, R.207, H.228, N.259, C.263, C.266, H.267, A.274, S.277, R.278, R.319, L.320, A.335, M.339, H.347 Ligands: HEC.2, HEC.6 12 PLIP interactions: 12 interactions with chain A, Hydrophobic interactions: A:E.203, A:R.207, A:R.278, A:L.320, A:A.335 Hydrogen bonds: A:Y.140, A:L.320 Salt bridges: A:K.141, A:R.278, A:R.278 Metal complexes: A:H.267, A:H.347 HEC.2: 18 residues within 4Å: Chain A: T.122, H.123, L.126, K.141, K.144, L.145, V.148, V.167, T.195, C.196, C.199, H.200, C.263, H.267, F.272, A.274 Ligands: HEC.1, HEC.4 14 PLIP interactions: 14 interactions with chain A, Hydrophobic interactions: A:T.122, A:L.145, A:V.148, A:V.167, A:H.267, A:F.272, A:F.272, A:A.274 Hydrogen bonds: A:T.122, A:A.274 Salt bridges: A:K.141, A:H.200 Metal complexes: A:H.123, A:H.200 HEC.3: 23 residues within 4Å: Chain A: Y.81, Y.88, P.91, S.93, P.94, A.98, E.99, D.102, C.103, C.106, H.107, E.110, C.169, I.170, H.173, V.174, H.184, I.188, M.190 Chain C: S.389, E.390, R.391 Ligands: HEC.4 17 PLIP interactions: 13 interactions with chain A, 4 interactions with chain C, Hydrophobic interactions: A:P.94, A:A.98, A:D.102, A:E.110, A:H.173, A:V.174, A:I.188, A:I.188 Hydrogen bonds: A:Y.88, A:Y.88, A:S.93, C:S.389, C:E.390, C:R.391 Metal complexes: A:H.107, A:H.184 Salt bridges: C:R.391 HEC.4: 26 residues within 4Å: Chain A: Y.81, P.84, H.107, T.111, W.114, V.115, W.118, H.123, V.167, G.168, C.169, C.172, H.173, M.190, P.191, K.262, D.264, R.269, H.270, F.272 Chain C: C.387, H.388, S.389, F.392 Ligands: HEC.2, HEC.3 15 PLIP interactions: 13 interactions with chain A, 2 interactions with chain C, Hydrophobic interactions: A:H.107, A:W.118, A:V.167, A:M.190, A:P.191, A:F.272, C:F.392 Salt bridges: A:K.262, A:R.269, A:R.269, A:H.270, C:H.388 pi-Stacking: A:W.114 Metal complexes: A:H.173, A:H.270 HEC.5: 22 residues within 4Å: Chain A: C.283, H.287, N.294, Y.298, H.303, P.332, T.333, C.334, C.337, H.338, K.352, T.353, R.354, W.355, A.356, W.380, M.400, A.482, H.483 Ligands: HEC.6, HEC.7, ISW.11 17 PLIP interactions: 17 interactions with chain A, Hydrophobic interactions: A:H.287, A:N.294, A:Y.298, A:Y.298, A:P.332, A:P.332, A:W.380, A:W.380, A:W.380, A:A.482 Hydrogen bonds: A:R.354, A:W.355, A:A.356 Salt bridges: A:R.354, A:H.478 pi-Stacking: A:H.338 Metal complexes: A:H.483 HEC.6: 25 residues within 4Å: Chain A: R.225, P.226, S.227, H.228, L.230, D.231, A.234, C.256, H.257, N.259, N.265, C.266, S.277, A.282, C.283, C.286, H.287, C.334, H.338, I.349, T.353, A.356 Ligands: HEC.1, HEC.5, ISW.11 13 PLIP interactions: 13 interactions with chain A, Hydrophobic interactions: A:N.265, A:H.338, A:I.349, A:I.349 Hydrogen bonds: A:P.226, A:S.227, A:S.227, A:T.353 Salt bridges: A:H.257 pi-Stacking: A:H.228, A:H.287 Metal complexes: A:H.228, A:H.287 HEC.7: 24 residues within 4Å: Chain A: H.303, L.306, F.324, N.330, A.331, P.332, T.383, C.384, Q.386, C.387, H.388, F.392, Y.396, L.397, V.484 Chain E: M.82, W.114, M.255, K.262, D.264, N.265, T.268, R.269 Ligands: HEC.5 23 PLIP interactions: 14 interactions with chain A, 9 interactions with chain E, Hydrophobic interactions: A:L.306, A:F.324, A:P.332, A:P.332, A:Q.386, A:F.392, A:F.392, A:Y.396, A:Y.396, A:L.397, A:V.484, A:V.484, E:W.114, E:R.269 Metal complexes: A:H.303, A:H.388 Hydrogen bonds: E:R.269 Water bridges: E:K.262, E:K.262 Salt bridges: E:K.262, E:K.262, E:R.269, E:R.269 HEC.12: 23 residues within 4Å: Chain C: Y.140, K.141, K.144, C.196, H.200, E.203, F.204, R.207, H.228, N.259, C.263, C.266, H.267, A.274, S.277, R.278, R.319, L.320, A.335, M.339, H.347 Ligands: HEC.13, HEC.17 15 PLIP interactions: 15 interactions with chain C, Hydrophobic interactions: C:H.200, C:E.203, C:F.204, C:R.207, C:A.274, C:R.278, C:L.320, C:A.335 Hydrogen bonds: C:Y.140, C:L.320 Salt bridges: C:K.141, C:R.278, C:R.278 Metal complexes: C:H.267, C:H.347 HEC.13: 21 residues within 4Å: Chain C: T.122, H.123, L.126, K.141, K.144, L.145, V.148, V.167, V.176, T.195, C.196, C.199, H.200, C.263, H.267, F.272, S.273, A.274, E.317 Ligands: HEC.12, HEC.15 15 PLIP interactions: 15 interactions with chain C, Hydrophobic interactions: C:T.122, C:L.145, C:V.167, C:V.167, C:V.176, C:H.267, C:F.272, C:F.272, C:A.274 Hydrogen bonds: C:A.274 Salt bridges: C:K.141, C:K.141, C:H.200 Metal complexes: C:H.123, C:H.200 HEC.14: 23 residues within 4Å: Chain C: Y.81, Y.88, P.91, S.93, P.94, E.96, A.98, E.99, D.102, C.103, C.106, H.107, E.110, C.169, I.170, H.173, V.174, H.184, I.188, M.190 Chain E: S.389, R.391 Ligands: HEC.15 15 PLIP interactions: 12 interactions with chain C, 3 interactions with chain E, Hydrophobic interactions: C:P.91, C:E.96, C:A.98, C:H.173, C:V.174, C:I.188, C:I.188 Hydrogen bonds: C:Y.88, C:Y.88, C:S.93, E:S.389, E:R.391 Metal complexes: C:H.107, C:H.184 Salt bridges: E:R.391 HEC.15: 26 residues within 4Å: Chain C: Y.81, P.84, H.107, T.111, W.114, V.115, W.118, H.123, V.167, G.168, C.169, C.172, H.173, M.190, P.191, K.262, D.264, R.269, H.270, F.272 Chain E: C.387, H.388, S.389, F.392 Ligands: HEC.13, HEC.14 15 PLIP interactions: 12 interactions with chain C, 3 interactions with chain E, Hydrophobic interactions: C:H.107, C:V.115, C:W.118, C:V.167, C:M.190, C:P.191, C:F.272, E:F.392 Salt bridges: C:R.269, C:R.269, E:H.388 pi-Stacking: C:W.114 Metal complexes: C:H.173, C:H.270 Hydrogen bonds: E:S.389 HEC.16: 22 residues within 4Å: Chain C: C.283, H.287, N.294, Y.298, H.303, P.332, T.333, C.334, C.337, H.338, K.352, T.353, R.354, W.355, A.356, W.380, M.400, A.482, H.483 Ligands: HEC.17, HEC.18, ISW.22 17 PLIP interactions: 17 interactions with chain C, Hydrophobic interactions: C:H.287, C:N.294, C:Y.298, C:Y.298, C:P.332, C:W.380, C:W.380, C:W.380, C:A.482 Hydrogen bonds: C:R.354, C:W.355, C:A.356 Water bridges: C:N.357 Salt bridges: C:R.354, C:H.478 Metal complexes: C:H.338, C:H.483 HEC.17: 25 residues within 4Å: Chain C: R.225, P.226, S.227, H.228, L.230, D.231, A.234, C.256, H.257, N.259, N.265, C.266, S.277, A.282, C.283, C.286, H.287, C.334, H.338, I.349, T.353, A.356 Ligands: HEC.12, HEC.16, ISW.22 12 PLIP interactions: 12 interactions with chain C, Hydrophobic interactions: C:H.338, C:I.349, C:I.349 Hydrogen bonds: C:P.226, C:S.227, C:S.227, C:T.353 Salt bridges: C:R.225 pi-Stacking: C:H.228, C:H.287 Metal complexes: C:H.228, C:H.287 HEC.18: 23 residues within 4Å: Chain A: W.114, M.255, K.262, D.264, T.268, R.269 Chain C: K.302, H.303, L.306, F.324, N.330, A.331, P.332, W.380, T.383, C.384, C.387, H.388, F.392, Y.396, L.397, V.484 Ligands: HEC.16 19 PLIP interactions: 12 interactions with chain C, 7 interactions with chain A, Hydrophobic interactions: C:F.324, C:P.332, C:P.332, C:F.392, C:Y.396, C:Y.396, C:L.397, C:V.484, C:V.484, A:W.114, A:R.269 pi-Stacking: C:H.388, C:F.392 Metal complexes: C:H.388 Hydrogen bonds: A:R.269 Salt bridges: A:K.262, A:K.262, A:R.269, A:R.269 HEC.23: 21 residues within 4Å: Chain E: Y.140, K.141, C.196, H.200, E.203, F.204, H.228, N.259, C.263, C.266, H.267, A.274, S.277, R.278, R.319, L.320, A.335, M.339, H.347 Ligands: HEC.24, HEC.28 12 PLIP interactions: 12 interactions with chain E, Hydrophobic interactions: E:H.200, E:E.203, E:E.203, E:R.278, E:A.335 Hydrogen bonds: E:Y.140, E:L.320 Salt bridges: E:K.141, E:R.278, E:R.278 Metal complexes: E:H.267, E:H.347 HEC.24: 20 residues within 4Å: Chain E: T.122, H.123, L.126, K.141, K.144, L.145, V.148, V.167, C.172, V.176, T.195, C.196, C.199, H.200, C.263, H.267, F.272, A.274 Ligands: HEC.23, HEC.26 15 PLIP interactions: 15 interactions with chain E, Hydrophobic interactions: E:L.126, E:L.145, E:V.148, E:V.167, E:V.176, E:H.267, E:F.272, E:F.272 Hydrogen bonds: E:T.122, E:K.141, E:A.274 Salt bridges: E:K.141, E:H.200 Metal complexes: E:H.123, E:H.200 HEC.25: 23 residues within 4Å: Chain A: S.389, E.390, R.391 Chain E: Y.81, Y.88, P.91, S.93, P.94, E.96, A.98, E.99, D.102, C.103, C.106, H.107, E.110, C.169, I.170, H.173, H.184, I.188, M.190 Ligands: HEC.26 13 PLIP interactions: 9 interactions with chain E, 4 interactions with chain A, Hydrophobic interactions: E:P.94, E:E.96, E:E.110, E:H.173, E:I.188 Hydrogen bonds: E:Y.88, E:Y.88, A:S.389, A:E.390, A:R.391 Metal complexes: E:H.107, E:H.184 Salt bridges: A:R.391 HEC.26: 25 residues within 4Å: Chain A: H.388, S.389, F.392 Chain E: Y.81, P.84, H.107, T.111, W.114, V.115, W.118, H.123, V.167, G.168, C.169, C.172, H.173, M.190, P.191, K.262, D.264, R.269, H.270, F.272 Ligands: HEC.24, HEC.25 15 PLIP interactions: 13 interactions with chain E, 2 interactions with chain A, Hydrophobic interactions: E:H.107, E:T.111, E:W.118, E:V.167, E:M.190, E:D.264, E:F.272, E:F.272 Salt bridges: E:R.269, E:R.269, A:H.388 pi-Stacking: E:W.114 Metal complexes: E:H.173, E:H.270 Hydrogen bonds: A:S.389 HEC.27: 22 residues within 4Å: Chain E: C.283, H.287, N.294, Y.298, H.303, P.332, T.333, C.334, C.337, H.338, K.352, T.353, R.354, W.355, A.356, W.380, M.400, A.482, H.483 Ligands: ISW.8, HEC.28, HEC.29 17 PLIP interactions: 17 interactions with chain E, Hydrophobic interactions: E:H.287, E:N.294, E:Y.298, E:Y.298, E:P.332, E:P.332, E:W.380, E:W.380, E:W.380, E:A.482 Hydrogen bonds: E:R.354, E:W.355, E:A.356 Salt bridges: E:R.354, E:H.478 pi-Stacking: E:H.338 Metal complexes: E:H.483 HEC.28: 24 residues within 4Å: Chain E: P.226, S.227, H.228, L.230, D.231, A.234, C.256, H.257, N.259, N.265, C.266, S.277, A.282, C.283, C.286, H.287, C.334, H.338, I.349, T.353, A.356 Ligands: ISW.8, HEC.23, HEC.27 11 PLIP interactions: 11 interactions with chain E, Hydrophobic interactions: E:P.226, E:N.265, E:H.338, E:I.349, E:I.349 Hydrogen bonds: E:S.227, E:T.353, E:A.356 Salt bridges: E:H.257 Metal complexes: E:H.228, E:H.287 HEC.29: 21 residues within 4Å: Chain C: W.114, M.255, K.262, D.264, T.268, R.269 Chain E: H.303, L.306, F.324, N.330, A.331, P.332, T.383, C.384, C.387, H.388, F.392, Y.396, L.397, V.484 Ligands: HEC.27 21 PLIP interactions: 10 interactions with chain C, 11 interactions with chain E, Hydrophobic interactions: C:W.114, C:T.268, C:R.269, E:F.324, E:P.332, E:P.332, E:F.392, E:Y.396, E:Y.396, E:L.397, E:V.484, E:V.484 Hydrogen bonds: C:R.269 Water bridges: C:K.262, C:K.262 Salt bridges: C:K.262, C:K.262, C:R.269, C:R.269 pi-Stacking: E:F.392 Metal complexes: E:H.388

3 x ISW: {3,3'-[(9S)-8,13-diethenyl-3,7,12,17-tetramethyl-9,10-dihydroporphyrin-2,18-diyl-kappa~4~N~21~,N~22~,N~23~,N~24~]dipropanoato(2-)}iron(Covalent)

ISW.8: 24 residues within 4Å: Chain A: G.487, T.490, Y.491 Chain E: W.221, R.225, A.234, N.235, T.238, W.241, C.253, C.256, H.257, T.285, C.286, H.287, S.288, H.292, N.294, N.357, Y.358, F.452 Ligands: HEC.27, HEC.28, JUG.30 16 PLIP interactions: 13 interactions with chain E, 2 interactions with chain A, 1 Ligand-Water interactions, Hydrophobic interactions: E:W.221, E:A.234, E:T.238, E:W.241, E:H.292, E:N.357, E:Y.358, E:F.452, A:Y.491, A:Y.491 Hydrogen bonds: E:N.294, E:N.294 Salt bridges: E:R.225 pi-Cation interactions: E:H.292 Metal complexes: E:H.257, H2O.4 ISW.11: 23 residues within 4Å: Chain A: W.221, R.225, A.234, N.235, T.238, W.241, G.252, C.253, C.256, H.257, T.285, C.286, H.287, H.292, N.294, N.357, Y.358, F.452 Chain C: T.490, Y.491 Ligands: HEC.5, HEC.6, PEG.10 15 PLIP interactions: 2 interactions with chain C, 12 interactions with chain A, 1 Ligand-Water interactions, Hydrophobic interactions: C:Y.491, C:Y.491, A:W.221, A:A.234, A:T.238, A:W.241, A:H.292, A:Y.358, A:F.452 Hydrogen bonds: A:N.294, A:N.294 Salt bridges: A:R.225 pi-Stacking: A:H.292 Metal complexes: A:H.257, H2O.1 ISW.22: 22 residues within 4Å: Chain C: W.221, R.225, A.234, N.235, T.238, W.241, C.253, C.256, H.257, T.285, C.286, H.287, H.292, N.294, N.357, Y.358, F.452 Chain E: T.490, Y.491 Ligands: HEC.16, HEC.17, JUG.19 14 PLIP interactions: 12 interactions with chain C, 2 interactions with chain E, Hydrophobic interactions: C:W.221, C:A.234, C:T.238, C:W.241, C:H.292, C:Y.358, C:F.452, E:Y.491, E:Y.491 Hydrogen bonds: C:N.294, C:N.294 Salt bridges: C:R.225 pi-Stacking: C:H.292 Metal complexes: C:H.257

3 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.9: 7 residues within 4Å: Chain A: F.360, Y.411, N.415, G.446, L.467, E.471 Ligands: PEG.10 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.411, A:N.415 PEG.10: 6 residues within 4Å: Chain A: Y.358, F.360, F.448, E.471 Ligands: PEG.9, ISW.11 No protein-ligand interaction detected (PLIP) PEG.31: 5 residues within 4Å: Chain E: F.360, Y.411, F.445, G.446 Ligands: JUG.30 No protein-ligand interaction detected (PLIP)

2 x JUG: 5-hydroxynaphthalene-1,4-dione(Non-covalent)

JUG.19: 6 residues within 4Å: Chain C: W.221, T.238, Y.358, F.448, E.471 Ligands: ISW.22 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:W.221, C:T.238, C:F.448, C:F.448 pi-Stacking: C:Y.358 JUG.30: 6 residues within 4Å: Chain E: T.238, Y.358, F.448, E.471 Ligands: ISW.8, PEG.31 3 PLIP interactions: 3 interactions with chain E Hydrophobic interactions: E:T.238 pi-Stacking: E:Y.358, E:F.448

2 x 1PE: PENTAETHYLENE GLYCOL(Non-functional Binders)

1PE.20: 6 residues within 4Å: Chain C: F.360, P.362, Y.411, N.415, G.446, L.467 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:P.362 Hydrogen bonds: C:Y.411, C:N.415 1PE.21: 5 residues within 4Å: Chain C: E.366, Q.412, A.416 Chain D: P.32, S.34 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fujiwara, T. et al., Enhancement of the activity of hydroxylamine oxidoreductase by juglone, plant secondary metabolite. To Be Published

Release Date

2021-03-10

Peptides

Aerobic hydroxylamine oxidoreductase: ACE
Uncharacterized protein: BDF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

E
E

B
B

D
D

F
F

Aerobic hydroxylamine oxidoreductase

Uncharacterized protein

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