SMTL ID : 6m0q.1 (1 other biounit)

Hydroxylamine oxidoreductase from Nitrosomonas europaea

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.99 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, 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, Y.345, H.347 Ligands: HEC.2, HEC.6 18 PLIP interactions: 18 interactions with chain A, Hydrophobic interactions: A:E.203, A:E.203, A:F.204, A:R.207, A:R.278, A:L.320, A:A.335 Hydrogen bonds: A:Y.140, A:L.320 Water bridges: A:R.278, A:R.278, A:K.321, A:Y.345 Salt bridges: A:K.141, A:R.278, A:R.278 Metal complexes: A:H.267, A:H.347 HEC.2: 20 residues within 4Å: Chain A: T.122, H.123, K.141, K.144, L.145, V.148, L.164, V.167, V.176, T.195, C.196, C.199, H.200, C.263, H.267, F.272, S.273, A.274 Ligands: HEC.1, HEC.4 21 PLIP interactions: 21 interactions with chain A, Hydrophobic interactions: A:K.144, A:L.145, A:V.148, A:V.167, A:V.167, A:V.176, A:V.176, A:H.267, A:F.272, A:F.272 Hydrogen bonds: A:T.122, A:A.274 Water bridges: A:T.122, A:T.122, A:A.275, A:R.278 Salt bridges: A:K.141, A:K.141, A:H.200 Metal complexes: A:H.123, A:H.200 HEC.3: 22 residues within 4Å: Chain A: Y.81, Y.88, S.93, P.94, E.96, A.98, D.102, C.103, C.106, H.107, E.110, C.169, I.170, H.173, A.182, H.184, I.188, M.190 Chain C: S.389, E.390, R.391 Ligands: HEC.4 20 PLIP interactions: 14 interactions with chain A, 6 interactions with chain C, Hydrophobic interactions: A:E.96, A:A.98, A:D.102, A:E.110, A:I.170, A:H.173, A:A.182, A:I.188, A:I.188 Hydrogen bonds: A:Y.88, A:Y.88, C:S.389, C:E.390, C:R.391 Water bridges: A:S.93, C:E.390, C:E.390 Metal complexes: A:H.107, A:H.184 Salt bridges: C:R.391 HEC.4: 25 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: H.388, S.389, F.392 Ligands: HEC.2, HEC.3 19 PLIP interactions: 16 interactions with chain A, 3 interactions with chain C, Hydrophobic interactions: A:H.107, A:T.111, A:V.115, A:W.118, A:M.190, A:D.264, A:F.272, C:F.392 Water bridges: A:R.269 Salt bridges: A:K.262, A:R.269, A:R.269, C:H.388 pi-Stacking: A:W.114, A:H.173, A:H.270 Metal complexes: A:H.173, A:H.270 Hydrogen bonds: C:S.389 HEC.5: 22 residues within 4Å: Chain A: C.283, H.287, N.294, W.295, Y.298, H.303, P.332, T.333, C.334, C.337, H.338, T.353, R.354, W.355, A.356, W.380, M.400, A.482, H.483 Ligands: HEC.6, HEC.7, ISW.8 24 PLIP interactions: 24 interactions with chain A, Hydrophobic interactions: A:H.287, A:N.294, A:W.295, A:Y.298, A:Y.298, A:Y.298, A:Y.298, A:P.332, A:P.332, A:T.353, A:W.380, A:W.380, A:W.380, A:A.482 Hydrogen bonds: A:R.354, A:W.355, A:A.356 Water bridges: A:N.357, A:N.357 Salt bridges: A:H.338, A:R.354 pi-Cation interactions: A:H.338 Metal complexes: A:H.338, A:H.483 HEC.6: 25 residues within 4Å: Chain A: R.225, P.226, S.227, H.228, D.231, A.234, M.255, 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.8 12 PLIP interactions: 12 interactions with chain A, Hydrophobic interactions: A:P.226, 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:R.225, A:H.257 Metal complexes: A:H.228, A:H.287 HEC.7: 22 residues within 4Å: Chain A: K.302, H.303, L.306, F.324, N.330, A.331, P.332, T.383, C.384, C.387, H.388, F.392, Y.396, V.484 Chain E: M.82, W.114, M.255, K.262, D.264, T.268, R.269 Ligands: HEC.5 22 PLIP interactions: 10 interactions with chain E, 12 interactions with chain A, Hydrophobic interactions: E:W.114, E:T.268, E:R.269, A:K.302, A:L.306, A:F.324, A:P.332, A:P.332, A:F.392, A:Y.396, A:Y.396, A:V.484 Hydrogen bonds: E:R.269 Water bridges: E:T.258, E:K.262 Salt bridges: E:K.262, E:K.262, E:R.269, E:R.269 pi-Stacking: A:F.392 Metal complexes: A:H.303, A:H.388 HEC.13: 22 residues within 4Å: Chain C: Y.140, K.141, 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.14, HEC.18 17 PLIP interactions: 17 interactions with chain C, Hydrophobic interactions: C:E.203, C:E.203, C:F.204, C:R.207, C:R.278, C:L.320, C:A.335 Hydrogen bonds: C:Y.140, C:L.320 Water bridges: C:Y.140, C:R.278, C:K.321 Salt bridges: C:K.141, C:R.278, C:R.278 Metal complexes: C:H.267, C:H.347 HEC.14: 21 residues within 4Å: Chain C: T.122, H.123, L.126, K.141, K.144, L.145, V.148, L.164, V.167, V.176, T.195, C.196, C.199, H.200, C.263, H.267, F.272, S.273, A.274 Ligands: HEC.13, HEC.16 21 PLIP interactions: 21 interactions with chain C, Hydrophobic interactions: C:L.126, C:K.144, C:L.145, C:V.148, C:L.164, C:V.167, C:V.176, C:V.176, C:H.267, C:F.272, C:F.272 Hydrogen bonds: C:T.122, C:T.122, C:A.274 Water bridges: C:T.122, C:R.278 Salt bridges: C:K.141, C:K.141, C:H.200 Metal complexes: C:H.123, C:H.200 HEC.15: 22 residues within 4Å: Chain C: Y.81, Y.88, P.91, S.93, P.94, E.96, A.98, D.102, C.103, C.106, H.107, E.110, C.169, I.170, H.173, H.184, I.188, M.190 Chain E: S.389, E.390, R.391 Ligands: HEC.16 20 PLIP interactions: 15 interactions with chain C, 5 interactions with chain E, Hydrophobic interactions: C:P.91, C:P.94, C:E.96, C:A.98, C:D.102, C:E.110, C:I.170, C:H.173, C:I.188, C:I.188 Hydrogen bonds: C:Y.88, C:Y.88, E:S.389, E:R.391 Water bridges: C:S.93, E:E.390, E:E.390 Metal complexes: C:H.107, C:H.184 Salt bridges: E:R.391 HEC.16: 25 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: H.388, S.389, F.392 Ligands: HEC.14, HEC.15 18 PLIP interactions: 14 interactions with chain C, 4 interactions with chain E, Hydrophobic interactions: C:H.107, C:V.115, C:W.118, C:M.190, C:F.272, C:F.272, E:F.392 Salt bridges: C:K.262, C:R.269, C:R.269, E:H.388 pi-Stacking: C:W.114, C:H.173, C:H.270 Metal complexes: C:H.173, C:H.270 Hydrogen bonds: E:S.389, E:S.389 HEC.17: 22 residues within 4Å: Chain C: C.283, H.287, N.294, W.295, Y.298, H.303, P.332, T.333, C.334, C.337, H.338, T.353, R.354, W.355, A.356, W.380, M.400, A.482, H.483 Ligands: HEC.18, HEC.19, ISW.20 22 PLIP interactions: 22 interactions with chain C, Hydrophobic interactions: C:H.287, C:N.294, C:W.295, C:Y.298, C:Y.298, C:Y.298, C:P.332, 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:H.338, C:R.354, C:H.478 pi-Cation interactions: C:H.338 Metal complexes: C:H.338, C:H.483 HEC.18: 25 residues within 4Å: Chain C: R.225, P.226, S.227, H.228, D.231, A.234, M.255, 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.13, HEC.17, ISW.20 12 PLIP interactions: 12 interactions with chain C, Hydrophobic interactions: C:P.226, 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, C:H.257 Metal complexes: C:H.228, C:H.287 HEC.19: 19 residues within 4Å: Chain A: W.114, K.262, D.264, T.268, R.269 Chain C: H.303, L.306, F.324, N.330, A.331, P.332, T.383, C.384, C.387, H.388, F.392, Y.396, V.484 Ligands: HEC.17 20 PLIP interactions: 11 interactions with chain C, 9 interactions with chain A, Hydrophobic interactions: C:L.306, C:F.324, C:P.332, C:P.332, C:F.392, C:Y.396, C:Y.396, C:V.484, A:W.114, A:R.269 pi-Stacking: C:F.392 Metal complexes: C:H.303, C:H.388 Hydrogen bonds: A:R.269 Water bridges: A:T.258, A:K.262 Salt bridges: A:K.262, A:K.262, A:R.269, A:R.269 HEC.24: 22 residues within 4Å: Chain E: Y.140, K.141, 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.25, HEC.29 18 PLIP interactions: 18 interactions with chain E, Hydrophobic interactions: E:E.203, E:E.203, E:F.204, E:R.207, E:R.278, E:L.320, E:A.335 Hydrogen bonds: E:Y.140, E:L.320 Water bridges: E:Y.140, E:R.278, E:K.321, E:Y.345 Salt bridges: E:K.141, E:R.278, E:R.278 Metal complexes: E:H.267, E:H.347 HEC.25: 20 residues within 4Å: Chain E: T.122, H.123, L.126, K.141, K.144, L.145, L.164, V.167, V.176, T.195, C.196, C.199, H.200, C.263, H.267, F.272, S.273, A.274 Ligands: HEC.24, HEC.27 18 PLIP interactions: 18 interactions with chain E, Hydrophobic interactions: E:T.122, E:L.126, E:K.144, E:L.145, E:V.167, E:V.176, E:H.267, E:F.272, E:F.272 Hydrogen bonds: E:T.122, E:A.274 Water bridges: E:A.275, E:E.317 Salt bridges: E:K.141, E:K.141, E:H.200 Metal complexes: E:H.123, E:H.200 HEC.26: 22 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, D.102, C.103, C.106, H.107, E.110, C.169, I.170, H.173, H.184, I.188, M.190 Ligands: HEC.27 18 PLIP interactions: 6 interactions with chain A, 12 interactions with chain E, Hydrogen bonds: A:S.389, A:S.389, A:S.389, A:E.390, A:R.391, E:Y.88 Salt bridges: A:R.391 Hydrophobic interactions: E:P.91, E:E.96, E:A.98, E:D.102, E:E.110, E:I.170, E:H.173, E:I.188, E:I.188 Metal complexes: E:H.107, E:H.184 HEC.27: 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.25, HEC.26 17 PLIP interactions: 14 interactions with chain E, 3 interactions with chain A, Hydrophobic interactions: E:H.107, E:T.111, E:W.118, E:M.190, E:D.264, E:F.272, E:F.272, A:F.392 Water bridges: E:R.269 Salt bridges: E:K.262, 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.28: 23 residues within 4Å: Chain E: C.283, H.287, N.294, W.295, Y.298, H.303, P.332, T.333, C.334, C.337, H.338, T.353, R.354, W.355, A.356, W.380, L.397, M.400, A.482, H.483 Ligands: ISW.9, HEC.29, HEC.30 23 PLIP interactions: 23 interactions with chain E, Hydrophobic interactions: E:H.287, E:N.294, E:Y.298, E:Y.298, E:Y.298, E:Y.298, E:P.332, E:P.332, E:W.380, E:W.380, E:L.397, E:A.482 Hydrogen bonds: E:R.354, E:W.355, E:A.356 Water bridges: E:H.338, E:T.353, E:N.357 Salt bridges: E:H.338, E:R.354 pi-Cation interactions: E:H.338 Metal complexes: E:H.338, E:H.483 HEC.29: 25 residues within 4Å: Chain E: R.225, P.226, S.227, H.228, D.231, A.234, M.255, 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.9, HEC.24, HEC.28 11 PLIP interactions: 11 interactions with chain E, Hydrophobic interactions: E:P.226, E:H.338, E:I.349 Hydrogen bonds: E:P.226, E:S.227, E:S.227, E:T.353 Salt bridges: E:R.225, E:H.257 Metal complexes: E:H.228, E:H.287 HEC.30: 23 residues within 4Å: Chain C: M.82, W.114, M.255, K.262, D.264, T.268, R.269 Chain E: K.302, 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.28 23 PLIP interactions: 10 interactions with chain C, 13 interactions with chain E, Hydrophobic interactions: C:W.114, C:T.268, C:R.269, E:K.302, E:L.306, E:F.324, E:P.332, E:P.332, E:F.392, E:Y.396, E:Y.396, E:L.397, E:V.484 Hydrogen bonds: C:R.269 Water bridges: C:T.258, 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.303, 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: 23 residues within 4Å: Chain A: W.221, R.225, P.226, 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.357, F.452 Chain C: G.487, T.490, Y.491 Ligands: HEC.5, HEC.6, PG4.12 12 PLIP interactions: 9 interactions with chain A, 2 interactions with chain C, 1 Ligand-Water interactions Hydrophobic interactions: A:W.221, A:P.226, A:T.238, A:W.241, A:F.452, A:F.452, C:Y.491, C:Y.491 Salt bridges: A:R.225 pi-Stacking: A:H.292 Metal complexes: A:H.257, H2O.11 ISW.9: 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, G.252, C.253, C.256, H.257, T.285, C.286, H.287, H.292, A.356, N.357, Y.358, F.452 Ligands: HEC.28, HEC.29, PGE.32 11 PLIP interactions: 8 interactions with chain E, 2 interactions with chain A, 1 Ligand-Water interactions, Hydrophobic interactions: E:W.221, E:T.238, E:W.241, E:F.452, E:F.452, A:Y.491, A:Y.491 Salt bridges: E:R.225 pi-Stacking: E:H.292 Metal complexes: E:H.257, H2O.8 ISW.20: 23 residues within 4Å: Chain C: 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.357, F.452 Chain E: P.486, G.487, T.490, Y.491 Ligands: HEC.17, HEC.18, PG4.23 12 PLIP interactions: 9 interactions with chain C, 2 interactions with chain E, 1 Ligand-Water interactions Hydrophobic interactions: C:W.221, C:T.238, C:W.241, C:F.452, C:F.452, E:Y.491, E:Y.491 Water bridges: C:N.294 Salt bridges: C:R.225 pi-Stacking: C:H.292 Metal complexes: C:H.257, H2O.27

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

PEG.10: 4 residues within 4Å: Chain A: P.75, I.76, A.77, F.87 No protein-ligand interaction detected (PLIP) PEG.21: 4 residues within 4Å: Chain C: P.75, I.76, I.80, F.87 No protein-ligand interaction detected (PLIP)

4 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.11: 6 residues within 4Å: Chain A: Y.422, E.423, G.425, Q.430, K.431, R.434 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.430, A:K.431 Water bridges: A:Y.422 PGE.22: 6 residues within 4Å: Chain C: Y.422, E.423, G.425, Q.430, K.431, R.434 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:Q.430, C:K.431 Water bridges: C:Y.422 PGE.31: 2 residues within 4Å: Chain E: D.109, E.110 No protein-ligand interaction detected (PLIP) PGE.32: 8 residues within 4Å: Chain E: W.221, T.238, Y.358, F.360, V.361, F.448, E.471 Ligands: ISW.9 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:T.238

3 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.12: 9 residues within 4Å: Chain A: W.221, E.237, T.238, Y.358, F.360, V.361, F.448, E.471 Ligands: ISW.8 2 PLIP interactions: 2 interactions with chain A Water bridges: A:R.225, A:E.237 PG4.23: 9 residues within 4Å: Chain C: W.221, E.237, T.238, Y.358, F.360, V.361, F.448, E.471 Ligands: ISW.20 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:E.237 Water bridges: C:R.225, C:R.225, C:R.225, C:T.239, C:T.239 PG4.33: 6 residues within 4Å: Chain E: T.86, F.87, Y.88, K.89, P.90, K.186 4 PLIP interactions: 4 interactions with chain E Hydrogen bonds: E:F.87, E:K.89, E:K.186 Water bridges: E:Y.88

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Akutsu, Y. et al., Juglone, a plant-derived 1,4-naphthoquinone, binds to hydroxylamine oxidoreductase and inhibits the electron transfer to cytochrome c 554. Appl.Environ.Microbiol. (2023)

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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