SMTL ID : 6ci0.2 (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

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

GLC-GLC.1: 4 residues within 4Å: Chain B: P.93, F.96, N.97, E.100 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.100 GLC-GLC.2: 4 residues within 4Å: Chain A: W.355 Chain B: F.66, H.68, N.69 No protein-ligand interaction detected (PLIP)

3 x TRD: TRIDECANE(Non-covalent)

TRD.3: 2 residues within 4Å: Chain A: L.64, W.65 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:W.65, A:W.65, A:W.65 TRD.10: 8 residues within 4Å: Chain A: T.381, H.456, F.457, R.460 Chain B: T.13, G.14, I.37, T.41 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:I.37, A:T.381, A:H.456, A:F.457 TRD.11: 7 residues within 4Å: Chain A: M.334, M.337, V.338 Chain B: L.84, V.85, G.88, L.92 5 PLIP interactions: 1 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:V.338, B:L.84, B:L.84, B:V.85, B:L.92

1 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 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:D.396, B:E.226, H2O.1, H2O.2, H2O.3

1 x CA: CALCIUM ION(Non-covalent)

CA.5: 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.1

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

CU.6: 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.2 CU.13: 5 residues within 4Å: Chain B: H.189, C.224, C.228, M.235 Ligands: CU.14 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.189, B:C.224, B:C.228 CU.14: 5 residues within 4Å: Chain B: C.224, E.226, C.228, H.232 Ligands: CU.13 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.224, B:E.226, B:C.228, B:H.232

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

HEA.7: 33 residues within 4Å: Chain A: 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, 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 32 PLIP interactions: 32 interactions with chain A, Hydrophobic interactions: A:V.29, A:V.29, A:T.32, A:I.83, A:M.90, A:V.95, A:A.98, A:F.404, A:M.408, A:V.413, A:V.413, A:I.416, A:I.420, A:T.451, A:F.452, A:A.485, A:F.492, A:F.492 Hydrogen bonds: A:T.32, A:R.36, A:W.156, A:Y.398, 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:H.405, A:F.452 Metal complexes: A:H.86, A:H.405 HEA.8: 30 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, I.347, F.375, T.376, 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, P.80 31 PLIP interactions: 27 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:T.343, A:I.347, 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:P.80 Hydrogen bonds: A:W.156, A:Y.272 Water bridges: A:D.396, A:D.396, A:R.465, A:R.465, A:R.466 Salt bridges: A:H.395, A:R.465, A:R.466 pi-Cation interactions: A:H.268, A:H.268, A:H.403 Metal complexes: A:H.403, H2O.2

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

DMU.9: 3 residues within 4Å: Chain B: S.145, P.146, E.149 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.145

1 x CD: CADMIUM ION(Non-covalent)

CD.12: 3 residues within 4Å: Chain B: E.252, H.255, H.257 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:E.252, B:E.252, B:H.255, B:H.257

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
C

B
D

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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