SMTL ID : 4fas.1

Complex crystal structure of hydroxylamine oxidoreductase and NE1300 from Nitrosomonas europaea

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

hetero-3-3-mer

Ligands

21 x HEC: HEME C(Covalent)

HEC.1: 20 residues within 4Å: Chain A: Y.57, Y.64, P.67, S.69, P.70, A.74, D.78, C.79, C.82, H.83, E.86, C.145, H.149, H.160, I.164, M.166 Chain C: S.365, E.366, R.367 Ligands: HEC.2 16 PLIP interactions: 10 interactions with chain A, 6 interactions with chain C, Hydrophobic interactions: A:P.67, A:P.70, A:D.78, A:E.86, A:H.149, A:I.164, A:I.164 Hydrogen bonds: A:Y.57, C:S.365, C:S.365, C:S.365, C:E.366, C:R.367 Metal complexes: A:H.83, A:H.160 Salt bridges: C:R.367 HEC.2: 24 residues within 4Å: Chain A: Y.57, P.60, H.83, W.90, V.91, W.94, H.99, V.143, G.144, C.145, C.148, H.149, M.166, P.167, K.238, D.240, R.245, H.246, F.248 Chain C: H.364, S.365, F.368 Ligands: HEC.1, HEC.3 16 PLIP interactions: 13 interactions with chain A, 3 interactions with chain C, Hydrophobic interactions: A:H.83, A:V.91, A:W.94, A:M.166, A:P.167, A:F.248, C:F.368 Water bridges: A:R.245 Salt bridges: A:K.238, A:R.245, A:R.245, C:H.364 pi-Stacking: A:W.90 Metal complexes: A:H.149, A:H.246 Hydrogen bonds: C:S.365 HEC.3: 19 residues within 4Å: Chain A: T.98, H.99, K.117, K.120, L.121, V.124, L.140, V.143, V.152, C.172, C.175, H.176, C.239, H.243, F.248, S.249, A.250 Ligands: HEC.2, HEC.4 19 PLIP interactions: 19 interactions with chain A, Hydrophobic interactions: A:K.120, A:L.121, A:V.124, A:L.140, A:V.143, A:V.143, A:V.152, A:F.248, A:F.248 Hydrogen bonds: A:T.98, A:F.248, A:A.250 Water bridges: A:T.98, A:A.251, A:R.254 Salt bridges: A:K.117, A:K.117 Metal complexes: A:H.99, A:H.176 HEC.4: 21 residues within 4Å: Chain A: Y.116, K.117, C.172, H.176, E.179, R.183, H.204, N.235, C.239, C.242, H.243, A.250, S.253, R.254, R.295, L.296, A.311, M.315, H.323 Ligands: HEC.3, HEC.5 17 PLIP interactions: 17 interactions with chain A, Hydrophobic interactions: A:H.176, A:E.179, A:E.179, A:R.183, A:R.254, A:L.296, A:A.311 Hydrogen bonds: A:L.296 Water bridges: A:R.254, A:R.254, A:K.297 Salt bridges: A:K.117, A:K.120, A:R.254, A:R.254 Metal complexes: A:H.243, A:H.323 HEC.5: 24 residues within 4Å: Chain A: R.201, P.202, S.203, H.204, D.207, A.210, C.232, H.233, N.235, N.241, C.242, S.253, A.258, C.259, C.262, H.263, C.310, H.314, I.325, T.329, A.332 Ligands: HEC.4, HEC.6, ISW.41 8 PLIP interactions: 8 interactions with chain A, Hydrophobic interactions: A:P.202, A:I.325 Hydrogen bonds: A:S.203, A:S.203 Salt bridges: A:R.201, A:H.233 Metal complexes: A:H.204, A:H.263 HEC.6: 22 residues within 4Å: Chain A: C.259, H.263, N.270, W.271, Y.274, H.279, P.308, T.309, C.310, C.313, H.314, T.329, R.330, W.331, A.332, W.356, M.376, A.458, H.459 Ligands: HEC.5, HEC.7, ISW.41 22 PLIP interactions: 22 interactions with chain A, Hydrophobic interactions: A:H.263, A:N.270, A:Y.274, A:Y.274, A:Y.274, A:Y.274, A:W.356, A:W.356, A:W.356, A:A.458 Hydrogen bonds: A:R.330, A:W.331, A:A.332 Water bridges: A:H.314, A:T.329, A:N.333, A:H.454 Salt bridges: A:H.314, A:R.330 pi-Cation interactions: A:H.314 Metal complexes: A:H.314, A:H.459 HEC.7: 21 residues within 4Å: Chain A: H.279, L.282, F.300, N.306, A.307, P.308, T.359, C.360, Q.362, C.363, H.364, F.368, Y.372, V.460 Chain B: W.90, M.231, K.238, D.240, T.244, R.245 Ligands: HEC.6 20 PLIP interactions: 9 interactions with chain B, 11 interactions with chain A, Hydrophobic interactions: B:W.90, B:R.245, A:L.282, A:F.300, A:P.308, A:Q.362, A:F.368, A:Y.372, A:Y.372, A:V.460 Hydrogen bonds: B:R.245 Water bridges: B:K.238, B:R.245 Salt bridges: B:K.238, B:K.238, B:R.245, B:R.245 pi-Stacking: A:F.368 Metal complexes: A:H.279, A:H.364 HEC.20: 21 residues within 4Å: Chain A: S.365, E.366, R.367 Chain B: Y.57, Y.64, S.69, P.70, E.72, A.74, D.78, C.79, C.82, H.83, E.86, C.145, I.146, H.149, H.160, I.164, M.166 Ligands: HEC.21 15 PLIP interactions: 10 interactions with chain B, 5 interactions with chain A, Hydrophobic interactions: B:P.70, B:E.72, B:D.78, B:E.86, B:I.146, B:H.149, B:I.164 Hydrogen bonds: B:Y.57, A:S.365, A:S.365, A:S.365, A:R.367 Metal complexes: B:H.83, B:H.160 Salt bridges: A:R.367 HEC.21: 24 residues within 4Å: Chain A: H.364, S.365, F.368 Chain B: Y.57, P.60, H.83, W.90, V.91, W.94, H.99, V.143, G.144, C.145, C.148, H.149, M.166, P.167, K.238, D.240, R.245, H.246, F.248 Ligands: HEC.20, HEC.22 14 PLIP interactions: 11 interactions with chain B, 3 interactions with chain A, Hydrophobic interactions: B:H.83, B:W.94, B:M.166, B:F.248, A:F.368 Water bridges: B:R.245 Salt bridges: B:K.238, B:R.245, B:R.245, A:H.364 pi-Stacking: B:W.90 Metal complexes: B:H.149, B:H.246 Hydrogen bonds: A:S.365 HEC.22: 19 residues within 4Å: Chain B: T.98, H.99, L.102, K.117, K.120, L.121, V.124, V.143, V.152, C.172, C.175, H.176, C.239, H.243, F.248, S.249, A.250 Ligands: HEC.21, HEC.23 20 PLIP interactions: 20 interactions with chain B, Hydrophobic interactions: B:L.102, B:K.120, B:L.121, B:V.124, B:V.143, B:V.143, B:V.152, B:V.152, B:F.248, B:F.248 Hydrogen bonds: B:T.98, B:F.248, B:A.250 Water bridges: B:T.98, B:A.251, B:R.254 Salt bridges: B:K.117, B:K.117 Metal complexes: B:H.99, B:H.176 HEC.23: 21 residues within 4Å: Chain B: Y.116, K.117, C.172, H.176, E.179, H.204, N.235, C.239, C.242, H.243, A.250, S.253, R.254, R.295, L.296, A.311, M.315, Y.321, H.323 Ligands: HEC.22, HEC.24 13 PLIP interactions: 13 interactions with chain B, Hydrophobic interactions: B:E.179, B:E.179, B:R.254, B:A.311 Hydrogen bonds: B:L.296 Water bridges: B:R.254, B:R.254, B:K.297 Salt bridges: B:K.117, B:R.254, B:R.254 Metal complexes: B:H.243, B:H.323 HEC.24: 24 residues within 4Å: Chain B: R.201, P.202, S.203, H.204, D.207, A.210, C.232, H.233, N.235, N.241, C.242, S.253, A.258, C.259, C.262, H.263, C.310, H.314, I.325, T.329, A.332 Ligands: ISW.8, HEC.23, HEC.25 7 PLIP interactions: 7 interactions with chain B, Hydrophobic interactions: B:P.202, B:I.325 Hydrogen bonds: B:S.203, B:S.203 Salt bridges: B:R.201 Metal complexes: B:H.204, B:H.263 HEC.25: 22 residues within 4Å: Chain B: C.259, H.263, N.270, W.271, Y.274, H.279, P.308, T.309, C.310, C.313, H.314, T.329, R.330, W.331, A.332, W.356, M.376, A.458, H.459 Ligands: ISW.8, HEC.24, HEC.26 22 PLIP interactions: 22 interactions with chain B, Hydrophobic interactions: B:H.263, B:N.270, B:Y.274, B:Y.274, B:Y.274, B:Y.274, B:P.308, B:P.308, B:T.329, B:W.356, B:W.356, B:W.356, B:A.458 Hydrogen bonds: B:R.330, B:W.331, B:A.332 Water bridges: B:N.333, B:H.454 Salt bridges: B:R.330 pi-Stacking: B:H.314 Metal complexes: B:H.314, B:H.459 HEC.26: 20 residues within 4Å: Chain B: K.278, H.279, L.282, F.300, N.306, A.307, P.308, T.359, C.360, C.363, H.364, F.368, Y.372, V.460 Chain C: W.90, K.238, D.240, T.244, R.245 Ligands: HEC.25 23 PLIP interactions: 11 interactions with chain C, 12 interactions with chain B, Hydrophobic interactions: C:W.90, C:T.244, C:R.245, B:K.278, B:L.282, B:F.300, B:P.308, B:P.308, B:F.368, B:Y.372, B:Y.372, B:V.460 Hydrogen bonds: C:R.245 Water bridges: C:T.234, C:K.238, C:R.245 Salt bridges: C:K.238, C:K.238, C:R.245, C:R.245 pi-Stacking: B:F.368 Metal complexes: B:H.279, B:H.364 HEC.42: 21 residues within 4Å: Chain B: S.365, E.366, R.367 Chain C: Y.57, Y.64, S.69, P.70, E.72, D.78, C.79, C.82, H.83, E.86, C.145, I.146, H.149, A.158, H.160, I.164, M.166 Ligands: HEC.43 15 PLIP interactions: 10 interactions with chain C, 5 interactions with chain B, Hydrophobic interactions: C:E.72, C:D.78, C:E.86, C:H.149, C:A.158, C:I.164, C:I.164 Hydrogen bonds: C:Y.57, B:S.365, B:S.365, B:E.366, B:R.367 Metal complexes: C:H.83, C:H.160 Salt bridges: B:R.367 HEC.43: 23 residues within 4Å: Chain B: H.364, S.365 Chain C: Y.57, P.60, H.83, W.90, V.91, W.94, H.99, V.143, G.144, C.145, C.148, H.149, M.166, P.167, K.238, D.240, R.245, H.246, F.248 Ligands: HEC.42, HEC.44 18 PLIP interactions: 15 interactions with chain C, 3 interactions with chain B, Hydrophobic interactions: C:H.83, C:V.91, C:W.94, C:M.166, C:F.248, C:F.248 Water bridges: C:R.245 Salt bridges: C:K.238, C:R.245, C:R.245, B:H.364 pi-Stacking: C:W.90, C:H.149, C:H.246 Metal complexes: C:H.149, C:H.246 Hydrogen bonds: B:S.365, B:S.365 HEC.44: 20 residues within 4Å: Chain C: T.98, H.99, K.117, K.120, L.121, V.124, L.140, V.143, V.152, T.171, C.172, C.175, H.176, C.239, H.243, F.248, S.249, A.250 Ligands: HEC.43, HEC.45 18 PLIP interactions: 18 interactions with chain C, Hydrophobic interactions: C:T.98, C:K.120, C:L.121, C:V.124, C:L.140, C:V.143, C:V.152, C:F.248, C:F.248 Hydrogen bonds: C:F.248, C:A.250 Water bridges: C:T.98, C:T.98, C:R.254 Salt bridges: C:K.117, C:K.117 Metal complexes: C:H.99, C:H.176 HEC.45: 23 residues within 4Å: Chain C: Y.116, K.117, K.120, C.172, H.176, E.179, F.180, H.204, N.235, C.239, C.242, H.243, A.250, S.253, R.254, R.295, L.296, A.311, M.315, Y.321, H.323 Ligands: HEC.44, HEC.46 16 PLIP interactions: 16 interactions with chain C, Hydrophobic interactions: C:E.179, C:E.179, C:F.180, C:A.250, C:R.254, C:L.296, C:A.311 Hydrogen bonds: C:L.296 Water bridges: C:R.254, C:R.254, C:K.297 Salt bridges: C:K.117, C:R.254, C:R.254 Metal complexes: C:H.243, C:H.323 HEC.46: 24 residues within 4Å: Chain C: R.201, P.202, S.203, H.204, D.207, A.210, M.231, C.232, H.233, N.235, N.241, C.242, A.258, C.259, C.262, H.263, C.310, H.314, I.325, T.329, A.332 Ligands: ISW.27, HEC.45, HEC.47 8 PLIP interactions: 8 interactions with chain C, Hydrophobic interactions: C:P.202, C:D.207, C:I.325 Hydrogen bonds: C:S.203, C:S.203 Salt bridges: C:R.201 Metal complexes: C:H.204, C:H.263 HEC.47: 22 residues within 4Å: Chain C: C.259, H.263, N.270, W.271, Y.274, H.279, P.308, T.309, C.310, C.313, H.314, T.329, R.330, W.331, A.332, W.356, M.376, A.458, H.459 Ligands: ISW.27, HEC.46, HEC.48 21 PLIP interactions: 21 interactions with chain C, Hydrophobic interactions: C:H.263, C:N.270, C:Y.274, C:Y.274, C:Y.274, C:Y.274, C:P.308, C:P.308, C:T.329, C:W.356, C:W.356, C:A.458 Hydrogen bonds: C:R.330, C:W.331, C:A.332 Water bridges: C:H.454 Salt bridges: C:H.314, C:R.330 pi-Cation interactions: C:H.314 Metal complexes: C:H.314, C:H.459 HEC.48: 20 residues within 4Å: Chain A: W.90, K.238, D.240, T.244, R.245 Chain C: K.278, H.279, L.282, F.300, N.306, A.307, P.308, T.359, C.360, C.363, H.364, F.368, Y.372, V.460 Ligands: HEC.47 20 PLIP interactions: 9 interactions with chain C, 11 interactions with chain A, Hydrophobic interactions: C:K.278, C:L.282, C:F.300, C:P.308, C:Y.372, C:Y.372, C:V.460, A:W.90, A:T.244, A:R.245 Metal complexes: C:H.279, C:H.364 Hydrogen bonds: A:R.245 Water bridges: A:K.238, A:R.245, A:R.245 Salt bridges: A:K.238, A:K.238, A:R.245, A:R.245

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: G.463, T.466, Y.467 Chain B: W.197, R.201, A.210, N.211, T.214, W.217, G.228, C.229, C.232, H.233, T.261, C.262, H.263, H.268, N.333, Y.334, F.428 Ligands: HEC.24, HEC.25, EDO.40 11 PLIP interactions: 2 interactions with chain A, 8 interactions with chain B, 1 Ligand-Water interactions, Hydrophobic interactions: A:Y.467, A:Y.467, B:W.197, B:A.210, B:T.214, B:W.217, B:F.428 Salt bridges: B:R.201 pi-Cation interactions: B:H.268 Metal complexes: B:H.233, H2O.1 ISW.27: 23 residues within 4Å: Chain B: G.463, T.466, Y.467 Chain C: W.197, R.201, A.210, N.211, T.214, W.217, G.228, C.229, C.232, H.233, T.261, C.262, H.263, H.268, N.333, Y.334, F.428 Ligands: HEC.46, HEC.47, PEG.50 12 PLIP interactions: 9 interactions with chain C, 2 interactions with chain B, 1 Ligand-Water interactions, Hydrophobic interactions: C:W.197, C:A.210, C:T.214, C:W.217, C:F.428, C:F.428, B:Y.467, B:Y.467 Salt bridges: C:R.201 pi-Cation interactions: C:H.268 Metal complexes: C:H.233, H2O.20 ISW.41: 24 residues within 4Å: Chain A: W.197, R.201, A.210, N.211, T.214, W.217, G.228, C.229, C.232, H.233, T.261, C.262, H.263, H.268, A.332, N.333, Y.334, F.428 Chain C: G.463, T.466, Y.467 Ligands: HEC.5, HEC.6, PEG.14 11 PLIP interactions: 8 interactions with chain A, 2 interactions with chain C, 1 Ligand-Water interactions, Hydrophobic interactions: A:W.197, A:A.210, A:T.214, A:W.217, A:F.428, C:Y.467, C:Y.467 Water bridges: A:R.201 Salt bridges: A:R.201 Metal complexes: A:H.233, H2O.20

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

PEG.9: 5 residues within 4Å: Chain A: P.51, I.52, A.53, I.56, F.63 Ligand excluded by PLIP PEG.10: 2 residues within 4Å: Chain A: H.38, G.39 Ligand excluded by PLIP PEG.11: 4 residues within 4Å: Chain A: N.449, E.469, P.473, R.476 Ligand excluded by PLIP PEG.12: 6 residues within 4Å: Chain A: S.110, D.111, D.112, P.113, K.302 Ligands: EDO.17 Ligand excluded by PLIP PEG.13: 5 residues within 4Å: Chain A: Y.398, E.399, G.401, Q.406, K.407 Ligand excluded by PLIP PEG.14: 3 residues within 4Å: Chain A: F.424, E.447 Ligands: ISW.41 Ligand excluded by PLIP PEG.28: 4 residues within 4Å: Chain B: R.96, T.98, N.101, K.104 Ligand excluded by PLIP PEG.29: 6 residues within 4Å: Chain B: S.3, V.5, P.6, D.7, R.17 Ligands: PG4.33 Ligand excluded by PLIP PEG.30: 5 residues within 4Å: Chain B: P.51, I.52, A.53, I.56, F.63 Ligand excluded by PLIP PEG.31: 5 residues within 4Å: Chain B: F.336, Y.387, N.391, G.422, L.443 Ligand excluded by PLIP PEG.49: 3 residues within 4Å: Chain C: G.119, E.122, N.126 Ligand excluded by PLIP PEG.50: 5 residues within 4Å: Chain C: T.214, Y.334, F.424, E.447 Ligands: ISW.27 Ligand excluded by PLIP PEG.51: 6 residues within 4Å: Chain C: G.132, K.133, L.134, G.135, E.138, K.155 Ligand excluded by PLIP PEG.52: 3 residues within 4Å: Chain C: R.76, K.141, E.142 Ligand excluded by PLIP PEG.53: 6 residues within 4Å: Chain A: E.86 Chain C: D.354, L.358, T.361, E.366, R.370 Ligand excluded by PLIP PEG.62: 5 residues within 4Å: Chain C: S.110, D.111, D.112, P.113, K.302 Ligand excluded by PLIP PEG.64: 5 residues within 4Å: Chain A: E.50 Chain F: V.30, K.32, R.44 Ligands: NO3.63 Ligand excluded by PLIP

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

PGE.15: 4 residues within 4Å: Chain A: R.96, T.98, N.101, K.104 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.104 PGE.54: 4 residues within 4Å: Chain C: R.96, T.98, N.101, K.104 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:K.104 Water bridges: C:T.98

15 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.16: 4 residues within 4Å: Chain A: D.16, K.19, A.20, E.24 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.16, A:E.24 EDO.17: 4 residues within 4Å: Chain A: D.298, S.301, K.302 Ligands: PEG.12 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.301, A:K.302 Water bridges: A:R.295, A:D.298 EDO.18: 4 residues within 4Å: Chain A: R.370, S.371, D.374 Chain B: A.53 No protein-ligand interaction detected (PLIP) EDO.19: 3 residues within 4Å: Chain A: T.215, P.416, K.418 No protein-ligand interaction detected (PLIP) EDO.34: 2 residues within 4Å: Chain B: S.371 Chain C: A.53 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.367 EDO.35: 3 residues within 4Å: Chain B: V.357, T.361, E.366 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain B Water bridges: C:E.86, B:E.366 EDO.38: 3 residues within 4Å: Chain B: A.37, H.38, T.209 1 PLIP interactions: 1 interactions with chain B Water bridges: B:A.199 EDO.39: 5 residues within 4Å: Chain B: Y.398, E.399, G.401, Q.406, K.407 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Y.398, B:E.399, B:K.407 Water bridges: B:Q.406 EDO.40: 4 residues within 4Å: Chain B: Y.334, F.424, E.447 Ligands: ISW.8 No protein-ligand interaction detected (PLIP) EDO.55: 3 residues within 4Å: Chain C: W.94, K.95, A.100 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:K.95, C:K.95 EDO.56: 3 residues within 4Å: Chain A: A.53 Chain C: R.370, S.371 No protein-ligand interaction detected (PLIP) EDO.57: 1 residues within 4Å: Chain C: K.19 No protein-ligand interaction detected (PLIP) EDO.58: 3 residues within 4Å: Chain C: Y.398, Q.406, K.407 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:Y.398, C:Q.406, C:K.407 EDO.60: 2 residues within 4Å: Chain C: P.51, F.63 No protein-ligand interaction detected (PLIP) EDO.61: 2 residues within 4Å: Chain C: A.37, H.38 No protein-ligand interaction detected (PLIP)

1 x P6G: HEXAETHYLENE GLYCOL(Non-functional Binders)

P6G.32: 6 residues within 4Å: Chain B: D.1, Y.115, Y.116, G.119, E.123, N.126 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.123

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

PG4.33: 3 residues within 4Å: Chain B: D.1, R.17 Ligands: PEG.29 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.17

4 x NO3: NITRATE ION(Non-functional Binders)

NO3.36: 4 residues within 4Å: Chain B: L.15, D.16, A.20, E.24 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.16, B:E.24 NO3.37: 4 residues within 4Å: Chain B: K.23, S.130, M.131, G.132 No protein-ligand interaction detected (PLIP) NO3.59: 3 residues within 4Å: Chain C: K.289, W.290, N.291 2 PLIP interactions: 2 interactions with chain C Water bridges: C:D.288, C:W.290 NO3.63: 5 residues within 4Å: Chain F: K.25, D.29, V.30, V.31 Ligands: PEG.64 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:K.25, F:K.25

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cedervall, P.E. et al., Structural studies of hydroxylamine oxidoreductase reveal a unique heme cofactor and a previously unidentified interaction partner. Biochemistry (2013)

Release Date

2013-09-04

Peptides

Hydroxylamine oxidoreductase: ABC
NE1300: DEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

Hydroxylamine oxidoreductase

NE1300

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