SMTL ID : 1ar1.1

Structure at 2.7 Angstrom Resolution of the Paracoccus Denitrificans two-subunit Cytochrome C Oxidase Complexed with an Antibody Fv Fragment

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

hetero-1-1-1-1-mer

Ligands

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

CU.1: 4 residues within 4Å: Chain A: H.276, H.325, H.326 Ligands: HEA.5 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.276, A:H.325, A:H.326 CU.12: 5 residues within 4Å: Chain B: C.245, E.247, C.249, H.253 Ligands: CU.13 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.245, B:E.247, B:C.249, B:H.253 CU.13: 5 residues within 4Å: Chain B: H.210, C.245, C.249, M.256 Ligands: CU.12 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.210, B:C.245, B:C.249

1 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 5 residues within 4Å: Chain A: H.403, D.404 Chain B: D.222, S.246, E.247 4 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: B:E.247, A:H.403, A:D.404, H2O.1

1 x CA: CALCIUM ION(Non-covalent)

CA.3: 6 residues within 4Å: Chain A: E.56, H.59, P.60, G.61, Q.63, D.477 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:E.56, A:E.56, A:H.59, A:G.61

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

HEA.4: 32 residues within 4Å: Chain A: L.36, V.47, T.50, M.53, R.54, W.87, I.91, H.94, G.95, M.98, M.99, V.102, V.103, A.106, G.163, W.164, Y.406, V.409, F.412, H.413, M.416, S.417, V.421, M.452, F.460, Q.463, R.473, R.474, Y.475, S.496, F.500, F.503 32 PLIP interactions: 32 interactions with chain A, Hydrophobic interactions: A:V.47, A:T.50, A:I.91, A:M.98, A:V.102, A:V.103, A:A.106, A:W.164, A:V.409, A:F.412, A:M.416, A:V.421, A:V.421, A:F.500, A:F.500, A:F.500, A:F.500, A:F.503 Hydrogen bonds: A:T.50, A:T.50, A:R.54, A:W.164, A:Y.406, A:Q.463, A:R.474, A:Y.475 Water bridges: A:R.473 Salt bridges: A:R.473, A:R.474 pi-Stacking: A:F.460 Metal complexes: A:H.94, A:H.413 HEA.5: 32 residues within 4Å: Chain A: W.164, W.272, V.279, Y.280, H.325, H.326, T.344, I.347, A.348, T.351, G.352, V.355, T.384, G.387, V.388, G.390, V.391, L.393, S.394, D.399, H.403, D.404, V.408, H.411, F.412, V.415, M.416, R.473 Chain B: V.74, P.114, L.118 Ligands: CU.1 28 PLIP interactions: 4 interactions with chain B, 24 interactions with chain A, Hydrophobic interactions: B:V.74, B:V.74, B:P.114, B:L.118, A:W.272, A:V.279, A:V.279, A:T.344, A:A.348, A:V.355, A:T.384, A:V.391, A:L.393, A:L.393, A:V.408, A:F.412, A:F.412, A:V.415 Hydrogen bonds: A:Y.280, A:Y.280, A:D.404 Water bridges: A:H.326 Salt bridges: A:H.403, A:R.473, A:R.474 pi-Stacking: A:H.325 pi-Cation interactions: A:H.276 Metal complexes: A:H.411

9 x LDA: LAURYL DIMETHYLAMINE-N-OXIDE(Non-covalent)

LDA.6: 3 residues within 4Å: Chain A: F.369, Q.446, W.450 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:W.450 LDA.7: 6 residues within 4Å: Chain A: I.359, W.363 Chain B: L.81, F.100, N.103, W.110 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:I.359, A:W.363, B:L.81, B:F.100, B:W.110 LDA.8: 6 residues within 4Å: Chain A: I.33, L.36, F.37, M.435, S.436, L.511 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:I.33, A:F.37, A:F.37, A:L.511 LDA.9: 6 residues within 4Å: Chain A: M.55, Q.58, H.59, Y.64, Y.494, F.497 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:Y.494, A:Y.494, A:F.497 Hydrogen bonds: A:Y.64 LDA.10: 3 residues within 4Å: Chain A: W.443, G.505, I.506 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:I.506 LDA.11: 3 residues within 4Å: Chain A: F.461 Ligands: LDA.14, LDA.15 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:F.461 LDA.14: 6 residues within 4Å: Chain A: F.461, H.464, F.465, R.468 Chain B: N.48 Ligands: LDA.11 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.461, A:F.465 LDA.15: 3 residues within 4Å: Chain A: F.461 Chain B: M.47 Ligands: LDA.11 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.461 pi-Cation interactions: A:Y.484 LDA.16: 7 residues within 4Å: Chain A: L.342 Chain B: V.115, L.118, V.119, A.123, L.126, P.127 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:V.115, B:L.118, A:L.342

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ostermeier, C. et al., Structure at 2.7 A resolution of the Paracoccus denitrificans two-subunit cytochrome c oxidase complexed with an antibody FV fragment. Proc.Natl.Acad.Sci.USA (1997)

Release Date

1998-02-11

Peptides

CYTOCHROME C OXIDASE: A
CYTOCHROME C OXIDASE: B
ANTIBODY FV FRAGMENT: C
ANTIBODY FV FRAGMENT: D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Membrane

We predict this structure to be a membrane protein.
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CYTOCHROME C OXIDASE

CYTOCHROME C OXIDASE

ANTIBODY FV FRAGMENT

ANTIBODY FV FRAGMENT

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