SMTL ID : 6ci0.1 (1 other biounit)

Catalytic core subunits (I and II) of cytochrome C oxidase from Rhodobacter sphaeroides with E101A (II) mutation

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

hetero-1-1-mer

Ligands

1 x GLC- GLC: alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose(Non-covalent)

GLC-GLC.1: 3 residues within 4Å: Chain B: P.93, F.96, E.100 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.100, B:E.100

5 x DMU: DECYL-BETA-D-MALTOPYRANOSIDE(Non-covalent)

DMU.2: 7 residues within 4Å: Chain A: V.15, L.18, F.19, M.427, S.428, P.529 Ligands: HEA.18 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.18, A:F.19, A:M.427 Water bridges: A:M.427 DMU.3: 8 residues within 4Å: Chain A: P.433, W.435, F.494, G.497, V.498, Y.501 Ligands: DMU.4, DMU.6 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:W.435, A:F.494, A:F.494, A:V.498, A:Y.501 DMU.4: 7 residues within 4Å: Chain A: W.435, L.439, A.490, F.494 Ligands: DMU.3, DMU.6, TRD.10 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.439, A:A.490, A:F.494 DMU.5: 10 residues within 4Å: Chain A: M.40, A.41, Q.45, F.46, S.67, A.68, V.69, F.486 Ligands: TRD.7, TRD.8 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:F.486, A:F.486 Hydrogen bonds: A:A.41, A:Q.45, A:Q.45, A:S.67 Water bridges: A:P.42, A:V.69 DMU.6: 6 residues within 4Å: Chain A: W.435, G.497, F.500, Y.501 Ligands: DMU.3, DMU.4 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:F.500

11 x TRD: TRIDECANE(Non-covalent)

TRD.7: 4 residues within 4Å: Chain A: L.64, W.65, P.66 Ligands: DMU.5 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:W.65, A:W.65, A:W.65, A:P.66 TRD.8: 5 residues within 4Å: Chain A: F.479, L.483, F.486, L.487 Ligands: DMU.5 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:F.479, A:L.483, A:F.486 TRD.9: 4 residues within 4Å: Chain A: L.361, L.366, L.369, K.438 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.361, A:L.366, A:L.369 TRD.10: 5 residues within 4Å: Chain A: W.435, K.438, L.439, W.442 Ligands: DMU.4 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:K.438, A:W.442 TRD.11: 2 residues within 4Å: Chain A: T.476, W.477 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:T.476 TRD.12: 4 residues within 4Å: Chain A: H.261, F.265, Q.328 Ligands: TRD.13 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:F.265 TRD.13: 7 residues within 4Å: Chain A: G.232, T.235, M.236, T.239, F.247, I.262 Ligands: TRD.12 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:T.235, A:T.239, A:F.247, A:I.262 TRD.14: 7 residues within 4Å: Chain A: A.30, F.31, Y.34, F.60, S.63, L.78, M.82 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:A.30, A:F.31, A:Y.34, A:Y.34, A:F.60, A:L.78 TRD.20: 5 residues within 4Å: Chain B: W.28, G.31, F.32, V.35, A.39 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:W.28, B:F.32, B:V.35, B:A.39 TRD.21: 8 residues within 4Å: Chain B: F.128, T.168, A.169, V.171, K.240, V.242, W.250, H.254 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:F.128, B:T.168, B:A.169, B:K.240, B:V.242, B:W.250 TRD.22: 5 residues within 4Å: Chain A: T.381, H.456, R.460 Chain B: T.13, G.14 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:T.381, A:H.456

3 x CU: COPPER (II) ION(Non-covalent)

CU.15: 3 residues within 4Å: Chain A: H.268, H.317, H.318 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.268, A:H.317, A:H.318, H2O.3 CU.24: 5 residues within 4Å: Chain B: C.224, E.226, C.228, H.232 Ligands: CU.25 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.224, B:E.226, B:C.228, B:H.232 CU.25: 5 residues within 4Å: Chain B: H.189, C.224, C.228, M.235 Ligands: CU.24 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.189, B:C.224, B:C.228

1 x MG: MAGNESIUM ION(Non-covalent)

MG.16: 4 residues within 4Å: Chain A: H.395, D.396 Chain B: S.225, E.226 5 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: A:H.395, B:E.226, H2O.1, H2O.4, H2O.5

1 x CA: CALCIUM ION(Non-covalent)

CA.17: 4 residues within 4Å: Chain A: E.38, A.41, G.43, Q.45 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.38, A:E.38, A:A.41, A:G.43, H2O.3

2 x HEA: HEME-A(Non-covalent)

HEA.18: 37 residues within 4Å: Chain A: G.21, G.22, V.29, T.32, M.35, R.36, W.79, I.83, H.86, M.90, M.91, V.94, V.95, A.98, G.155, W.156, Y.398, V.401, F.404, H.405, M.408, S.409, V.413, I.416, I.420, M.444, T.451, F.452, Q.455, R.465, R.466, Y.467, A.485, S.488, F.492, F.495 Ligands: DMU.2 31 PLIP interactions: 31 interactions with chain A, Hydrophobic interactions: A:V.29, A:T.32, A:I.83, A:M.90, A:V.95, A:A.98, A:V.401, A:F.404, A:F.404, A:M.408, A:V.413, A:I.416, A:I.420, A:T.451, A:F.452, A:A.485, A:F.492, A:F.495 Hydrogen bonds: A:T.32, A:R.36, A:W.156, A:Q.455, A:R.466, A:Y.467 Water bridges: A:R.465 Salt bridges: A:R.465, A:R.466 pi-Stacking: A:F.452 pi-Cation interactions: A:H.405 Metal complexes: A:H.86, A:H.405 HEA.19: 28 residues within 4Å: Chain A: W.156, W.264, V.271, Y.272, V.275, H.317, H.318, T.336, I.339, A.340, T.343, G.344, F.375, G.379, G.382, I.383, L.385, S.386, D.391, H.395, V.400, H.403, F.404, V.407, M.408, R.465 Chain B: I.40, L.84 27 PLIP interactions: 23 interactions with chain A, 3 interactions with chain B, 1 Ligand-Water interactions, Hydrophobic interactions: A:W.264, A:V.271, A:V.275, A:T.336, A:A.340, A:F.375, A:I.383, A:L.385, A:F.404, A:F.404, A:V.407, B:I.40, B:I.40, B:L.84 Hydrogen bonds: A:W.156, A:Y.272 Water bridges: A:H.318, A:D.396, A:D.396, A:R.465, A:R.465 Salt bridges: A:H.395, A:R.465, A:R.466 pi-Cation interactions: A:H.268 Metal complexes: A:H.403, H2O.3

1 x CD: CADMIUM ION(Non-covalent)

CD.23: 3 residues within 4Å: Chain B: E.252, H.255, H.257 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:E.252, B:E.252, B:H.257

3 x HTH: (2S,3R)-heptane-1,2,3-triol(Non-covalent)

HTH.26: 5 residues within 4Å: Chain B: E.124, A.248, L.251, E.252, H.255 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:L.251, B:E.252 Hydrogen bonds: B:E.124 HTH.27: 7 residues within 4Å: Chain A: M.334, M.337, V.338 Chain B: L.84, V.85, G.88, A.89 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:V.85, B:G.88 Hydrophobic interactions: A:V.338 HTH.28: 6 residues within 4Å: Chain A: Y.297, L.298, P.299 Chain B: H.68, S.70, I.74 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.298

1 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.29: 4 residues within 4Å: Chain B: S.127, F.128, E.129 Ligands: K.30 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.129 Water bridges: B:E.129, B:E.129

1 x K: POTASSIUM ION(Non-functional Binders)

K.30: 1 residues within 4Å: Ligands: TRS.29 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hiser, C. et al., The K-path entrance in cytochrome c oxidase is defined by mutation of E101 and controlled by an adjacent ligand binding domain. Biochim. Biophys. Acta (2018)

Release Date

2018-04-25

Peptides

Cytochrome c oxidase subunit 1: A
Cytochrome c oxidase subunit 2: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Membrane

We predict this structure to be a membrane protein.
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Cytochrome c oxidase subunit 1

Cytochrome c oxidase subunit 2

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