SMTL ID : 1qle.1

CRYO-STRUCTURE OF THE PARACOCCUS DENITRIFICANS FOUR-SUBUNIT CYTOCHROME C OXIDASE IN THE COMPLETELY OXIDIZED STATE COMPLEXED WITH AN ANTIBODY FV FRAGMENT

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.00 Å

Oligo State

hetero-1-1-1-1-1-1-mer

Ligands

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

HEA.1: 30 residues within 4Å: Chain A: L.20, A.23, G.24, V.31, T.34, M.37, R.38, W.71, I.75, H.78, M.82, M.83, V.86, V.87, A.90, G.147, W.148, Y.390, V.393, F.396, H.397, M.400, S.401, V.405, M.436, R.457, R.458, Y.459, S.480, F.484 29 PLIP interactions: 29 interactions with chain A, Hydrophobic interactions: A:A.23, A:V.31, A:V.31, A:T.34, A:I.75, A:M.82, A:V.86, A:V.87, A:A.90, A:V.393, A:F.396, A:F.396, A:M.400, A:V.405, A:F.484, A:F.484, A:F.484 Hydrogen bonds: A:T.34, A:I.75, A:W.148, A:Q.447, A:R.458, A:Y.459 Salt bridges: A:R.457, A:R.458 pi-Stacking: A:F.396, A:F.444 Metal complexes: A:H.78, A:H.397 HEA.2: 29 residues within 4Å: Chain A: W.148, W.256, V.263, Y.264, H.309, H.310, T.328, I.331, A.332, T.335, G.336, T.368, G.371, V.372, G.374, V.375, L.377, S.378, D.383, H.387, V.392, H.395, F.396, V.399, M.400, R.457, R.458 Chain B: V.45, I.88 19 PLIP interactions: 16 interactions with chain A, 3 interactions with chain B, Hydrophobic interactions: A:W.256, A:V.263, A:T.328, A:A.332, A:V.375, A:V.392, A:F.396, A:F.396, A:V.399, B:V.45, B:V.45, B:I.88 Hydrogen bonds: A:Y.264, A:D.383 Salt bridges: A:H.387, A:R.457, A:R.458 pi-Cation interactions: A:H.260 Metal complexes: A:H.395

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

CU.3: 3 residues within 4Å: Chain A: H.260, H.309, H.310 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.260, A:H.309, A:H.310

1 x CA: CALCIUM ION(Non-covalent)

CA.4: 5 residues within 4Å: Chain A: E.40, H.43, P.44, G.45, Q.47 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:E.40, A:E.40, A:H.43, A:G.45

1 x MN: MANGANESE (II) ION(Non-covalent)

MN.5: 3 residues within 4Å: Chain A: H.387, D.388 Chain B: E.218 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Metal complexes: A:H.387, A:D.388, B:E.218

1 x CUA: DINUCLEAR COPPER ION(Non-covalent)

CUA.6: 6 residues within 4Å: Chain B: H.181, C.216, E.218, C.220, H.224, M.227 6 PLIP interactions: 6 interactions with chain B Metal complexes: B:H.181, B:C.216, B:C.216, B:C.220, B:C.220, B:H.224

2 x PC1: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE(Non-covalent)

PC1.7: 20 residues within 4Å: Chain A: L.217, F.257, F.304, V.305, W.307, G.315, Q.320, Y.323, F.324 Chain B: R.198 Chain C: M.99, V.102, W.106, K.110, Y.114, P.121, D.124 Chain D: S.31, L.35, N.42 16 PLIP interactions: 5 interactions with chain C, 8 interactions with chain A, 1 interactions with chain B, 2 interactions with chain D Hydrophobic interactions: C:V.102, C:W.106, A:L.217, A:F.257, A:F.304, A:V.305, A:W.307, A:Y.323, A:Y.323, A:F.324, D:L.35 Salt bridges: C:K.110, C:D.124, B:R.198 pi-Cation interactions: C:Y.114 Hydrogen bonds: D:N.42 PC1.8: 23 residues within 4Å: Chain C: L.55, L.59, M.62, W.66, V.69, V.70, G.73, E.74, H.78, L.86, F.90, I.222, I.225, F.226, V.229, R.233, Q.238, M.239, T.240, Q.243, H.244, V.245, G.246 20 PLIP interactions: 20 interactions with chain C Hydrophobic interactions: C:L.55, C:L.59, C:W.66, C:W.66, C:L.86, C:F.90, C:F.90, C:I.222, C:I.225, C:F.226, C:F.226, C:F.226, C:F.226, C:V.229 Hydrogen bonds: C:V.245, C:G.246 Salt bridges: C:E.74, C:H.78, C:H.78, C:R.233

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Harrenga, A. et al., The Cytochrome C Oxidase from Paracoccus Denitrificans Does not Change the Metal Center Ligation Upon Reduction. J.Biol.Chem. (1999)

Release Date

1999-12-02

Peptides

CYTOCHROME C OXIDASE POLYPEPTIDE I-BETA: A
CYTOCHROME C OXIDASE POLYPEPTIDE II: B
CYTOCHROME C OXIDASE POLYPEPTIDE III: C
CCYTOCHROME C OXIDASE: D
HEAVY CHAIN ANTIBODY FV FRAGMENT: E
LIGHT CHAIN ANTIBODY FV FRAGMENT: F

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
H

F
L

Membrane

We predict this structure to be a membrane protein.
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CYTOCHROME C OXIDASE POLYPEPTIDE I-BETA

CYTOCHROME C OXIDASE POLYPEPTIDE II

CYTOCHROME C OXIDASE POLYPEPTIDE III

CCYTOCHROME C OXIDASE

HEAVY CHAIN ANTIBODY FV FRAGMENT

LIGHT CHAIN ANTIBODY FV FRAGMENT