SMTL ID : 5iy5.1 (1 other biounit)

Electron transfer complex of cytochrome c and cytochrome c oxidase at 2.0 angstrom resolution

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

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

Ligands

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

CU.1: 4 residues within 4Å: Chain A: H.240, H.290, H.291 Ligands: PER.6 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.240, A:H.290, A:H.291

1 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: H.368, D.369 Chain B: S.197, E.198 6 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: B:E.198, A:H.368, A:D.369, H2O.11, H2O.12, H2O.15

2 x NA: SODIUM ION(Non-functional Binders)

NA.3: 4 residues within 4Å: Chain A: E.40, Q.43, G.45, S.441 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.40 Water bridges: A:Q.43 NA.13: 4 residues within 4Å: Chain C: H.146, M.150, H.230, E.234 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:H.146, C:E.234

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

HEA.4: 33 residues within 4Å: Chain A: A.24, G.27, T.31, S.34, I.37, R.38, Y.54, V.58, H.61, A.62, M.65, I.66, M.69, V.70, I.73, G.125, W.126, Y.371, V.374, F.377, H.378, L.381, S.382, V.386, F.393, F.425, Q.428, R.438, R.439, Y.440, S.458, V.465, M.468 30 PLIP interactions: 30 interactions with chain A, Hydrophobic interactions: A:A.24, A:R.38, A:V.58, A:V.58, A:A.62, A:M.65, A:I.66, A:V.70, A:V.374, A:L.381, A:L.381, A:F.393, A:F.393, A:F.425 Hydrogen bonds: A:R.38, A:W.126, A:S.382, A:Q.428, A:R.439, A:Y.440 Water bridges: A:R.438, A:R.438, A:S.461 Salt bridges: A:R.438, A:R.439 pi-Stacking: A:H.61, A:F.377, A:F.425 Metal complexes: A:H.61, A:H.378 HEA.5: 34 residues within 4Å: Chain A: W.126, W.236, V.243, Y.244, I.247, H.290, H.291, T.309, I.312, A.313, T.316, G.317, V.320, F.348, T.349, G.352, L.353, G.355, I.356, L.358, A.359, D.364, H.368, V.373, H.376, F.377, V.380, L.381, R.438 Chain B: I.34, P.69, I.72, L.73 Ligands: PER.6 38 PLIP interactions: 34 interactions with chain A, 4 interactions with chain B, Hydrophobic interactions: A:W.236, A:V.243, A:V.243, A:V.243, A:I.247, A:I.247, A:T.309, A:A.313, A:T.316, A:V.320, A:F.348, A:L.353, A:I.356, A:I.356, A:L.358, A:V.373, A:V.373, A:F.377, A:F.377, A:V.380, A:L.381, A:L.381, A:L.381, B:I.34, B:P.69, B:I.72, B:L.73 Hydrogen bonds: A:W.126, A:Y.244, A:Y.244 Water bridges: A:T.316, A:D.369, A:D.369, A:R.439 Salt bridges: A:H.368, A:R.438, A:R.439 Metal complexes: A:H.376

1 x PER: PEROXIDE ION(Non-covalent)

PER.6: 6 residues within 4Å: Chain A: H.240, V.243, H.290, H.291 Ligands: CU.1, HEA.5 No protein-ligand interaction detected (PLIP)

4 x PGV: (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE(Non-covalent)

PGV.7: 9 residues within 4Å: Chain A: N.406, T.408, W.409 Chain D: F.84 Chain K: F.4, H.5 Chain M: P.12, Q.15, A.16 8 PLIP interactions: 3 interactions with chain A, 1 interactions with chain K, 3 interactions with chain M, 1 interactions with chain D Hydrophobic interactions: A:W.409, A:W.409, K:F.4, M:P.12, M:P.12, D:F.84 Water bridges: A:R.480, M:A.6 PGV.8: 29 residues within 4Å: Chain A: F.94, P.95, R.96, M.97, F.148, L.152, V.155, L.159, P.200 Chain C: H.7, V.9, G.18, A.22, T.26, N.48, T.51, M.52, W.55, W.56, V.59, E.62, H.69, L.77, G.80, F.84, S.87, F.91 Ligands: PEK.14, PGV.15 20 PLIP interactions: 12 interactions with chain C, 8 interactions with chain A Hydrophobic interactions: C:A.22, C:T.26, C:T.51, C:W.55, C:W.55, C:W.55, C:W.56, C:F.84, C:F.91, A:F.148, A:L.152, A:V.155, A:L.159, A:P.200 Hydrogen bonds: C:H.7, C:E.62, A:R.96, A:M.97 Water bridges: C:M.81 Salt bridges: A:R.96 PGV.15: 24 residues within 4Å: Chain C: M.49, M.52, W.56, V.59, I.60, S.63, T.64, H.69, M.81, F.84, E.88, H.205, I.208, F.212, R.219, H.224, F.225, T.226, H.229, H.230, F.231, G.232 Ligands: PGV.8, CDL.17 26 PLIP interactions: 2 interactions with chain F, 24 interactions with chain C Water bridges: F:Q.12, F:E.17, C:S.63, C:R.219, C:T.226, C:H.229 Hydrophobic interactions: C:W.56, C:W.56, C:W.56, C:W.56, C:W.56, C:W.56, C:I.60, C:F.84, C:I.208, C:I.208, C:F.212, C:F.212 Hydrogen bonds: C:S.63, C:H.69, C:R.219, C:F.231, C:G.232 Salt bridges: C:R.219, C:R.219, C:H.229 PGV.16: 11 residues within 4Å: Chain A: F.237, D.298 Chain C: T.93, W.97, Y.100, H.101, L.104, A.105 Chain H: N.16, N.18 Ligands: CHD.12 7 PLIP interactions: 2 interactions with chain H, 1 interactions with chain B, 3 interactions with chain C, 1 interactions with chain A Hydrogen bonds: H:N.16 Water bridges: H:N.18, B:R.178 Hydrophobic interactions: C:T.93, C:W.97, C:W.97, A:F.237

3 x TGL: TRISTEAROYLGLYCEROL(Non-covalent)

TGL.9: 17 residues within 4Å: Chain A: V.350, Y.379, N.422, F.426, H.429, F.430, L.433, W.450 Chain B: L.7, G.8, L.28, V.31, F.32, S.35, S.36, L.39 Chain I: R.43 18 PLIP interactions: 9 interactions with chain B, 8 interactions with chain A, 1 interactions with chain I Hydrophobic interactions: B:L.7, B:L.28, B:V.31, B:F.32, B:F.32, B:L.39, A:V.350, A:F.426, A:F.426, A:F.426, A:H.429, A:F.430, A:F.430, A:W.450 Water bridges: B:G.8, B:F.9 Salt bridges: B:H.24, I:R.43 TGL.23: 20 residues within 4Å: Chain A: W.334, M.339, L.342, G.343, F.414, A.415 Chain B: L.39, I.42, L.46, T.47, K.49 Chain D: R.70, S.71, T.72, E.74, W.75, M.83, I.86 Chain I: R.16, H.20 14 PLIP interactions: 7 interactions with chain A, 4 interactions with chain B, 3 interactions with chain D Hydrophobic interactions: A:W.334, A:W.334, A:L.342, A:F.414, A:A.415, B:L.39, B:I.42, B:L.46, B:T.47, D:E.74, D:I.86 Water bridges: A:K.411 Salt bridges: A:K.411 Hydrogen bonds: D:E.74 TGL.34: 23 residues within 4Å: Chain A: T.17, L.21, F.22, W.25, W.81, P.106, L.113, F.393, F.400, S.401, I.472 Chain L: N.9, I.10, P.11, F.12, S.13, R.19, M.23, M.24, L.26, F.27, F.28, S.30 23 PLIP interactions: 13 interactions with chain A, 10 interactions with chain L Hydrophobic interactions: A:T.17, A:L.21, A:L.21, A:L.21, A:F.22, A:W.25, A:W.25, A:W.25, A:W.81, A:L.113, A:F.393, A:F.400, A:I.472, L:I.10, L:P.11, L:F.12, L:F.12, L:F.12, L:L.26, L:F.27, L:F.27, L:F.28, L:F.28

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

CUA.10: 6 residues within 4Å: Chain B: H.161, C.196, E.198, C.200, H.204, M.207 7 PLIP interactions: 7 interactions with chain B Metal complexes: B:H.161, B:C.196, B:C.196, B:E.198, B:C.200, B:C.200, B:H.204

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

EDO.11: 7 residues within 4Å: Chain A: Y.447 Chain B: M.1, A.2, Q.10, L.136, P.166, Y.193 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:A.2, B:Q.10, B:Y.193, A:Y.447 EDO.22: 4 residues within 4Å: Chain A: A.223 Chain B: G.177 Chain C: E.109 Chain H: W.62 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain H Hydrogen bonds: B:G.177, H:W.62 EDO.25: 2 residues within 4Å: Chain E: E.98, E.99 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:E.98 Water bridges: E:G.101 EDO.27: 3 residues within 4Å: Chain C: H.229 Chain F: D.9, E.17 5 PLIP interactions: 3 interactions with chain F, 2 interactions with chain C Hydrogen bonds: F:E.17, C:N.228, C:H.229 Water bridges: F:D.9, F:E.17 EDO.30: 6 residues within 4Å: Chain C: G.118 Chain G: A.46, F.47, I.48, L.53, R.54 5 PLIP interactions: 4 interactions with chain G, 1 interactions with chain C Hydrogen bonds: G:I.48, G:I.48, G:R.54, G:R.54, C:G.118 EDO.31: 5 residues within 4Å: Chain I: Y.54, D.55, K.58, D.59, E.62 3 PLIP interactions: 3 interactions with chain I Hydrogen bonds: I:D.55, I:D.55, I:K.58

4 x CHD: CHOLIC ACID(Non-covalent)

CHD.12: 9 residues within 4Å: Chain A: H.233, W.288, D.300, T.301, Y.304, F.305 Chain C: W.97, H.101 Ligands: PGV.16 9 PLIP interactions: 7 interactions with chain A, 2 interactions with chain C Hydrophobic interactions: A:W.288, A:Y.304, C:W.97 Hydrogen bonds: A:T.301 Water bridges: A:H.233, A:H.233, A:T.301 Salt bridges: A:H.233, C:H.101 CHD.18: 8 residues within 4Å: Chain C: R.154, L.158, Q.159, F.162, F.217, L.221 Chain J: F.1 Ligands: UNL.20 8 PLIP interactions: 6 interactions with chain C, 2 interactions with chain J Hydrophobic interactions: C:F.162, C:F.162, C:F.217, C:L.221, J:F.1 Hydrogen bonds: C:Q.159, J:F.1 Salt bridges: C:R.154 CHD.29: 5 residues within 4Å: Chain G: R.14, R.17, F.18, F.21, G.22 3 PLIP interactions: 3 interactions with chain G Water bridges: G:R.17 Salt bridges: G:R.14, G:R.17 CHD.32: 7 residues within 4Å: Chain A: I.3, L.7 Chain J: Y.32, R.33, M.36, T.37, L.40 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain J Hydrophobic interactions: A:I.3, J:R.33, J:M.36 Hydrogen bonds: J:R.33

1 x PEK: (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(STEAROYLOXY)METHYL]ETHYL (5E,8E,11E,14E)-ICOSA-5,8,11,14-TETRAENOATE(Non-covalent)

PEK.14: 24 residues within 4Å: Chain A: H.151, V.155, A.203, T.207, L.210, L.215 Chain C: W.32, A.176, Y.179, Y.180, A.182, F.184, T.185, I.186, F.196, G.200, G.203 Chain G: W.62, T.68, F.69, F.70, H.71, N.76 Ligands: PGV.8 14 PLIP interactions: 5 interactions with chain G, 5 interactions with chain C, 4 interactions with chain A Hydrophobic interactions: G:F.69, C:W.32, C:A.176, C:Y.179, A:V.155, A:A.203, A:L.210, A:L.215 Hydrogen bonds: G:T.68, G:F.70, G:N.76, C:Y.179, C:I.186 Water bridges: G:F.69

2 x CDL: CARDIOLIPIN(Non-covalent)

CDL.17: 23 residues within 4Å: Chain C: M.49, L.50, M.52, Y.53, W.56, R.57, I.60, R.61, F.65, T.172, I.207, T.211, I.214, V.215, F.218, R.219, K.222, H.224 Chain J: K.8, D.28, I.30, L.31 Ligands: PGV.15 24 PLIP interactions: 3 interactions with chain J, 21 interactions with chain C Hydrophobic interactions: J:I.30, C:M.49, C:Y.53, C:Y.53, C:Y.53, C:W.56, C:R.57, C:T.172, C:I.207, C:T.211, C:I.214, C:I.214, C:V.215, C:V.215, C:F.218 Hydrogen bonds: J:D.28, C:Y.53 Salt bridges: J:K.8, C:R.61, C:K.222, C:H.224 Water bridges: C:R.61, C:R.61, C:K.222 CDL.28: 12 residues within 4Å: Chain C: L.125, L.129, V.140, L.248 Chain G: L.23, A.24, S.27, L.30, C.31, N.34, L.37, H.38 8 PLIP interactions: 3 interactions with chain C, 5 interactions with chain G Hydrophobic interactions: C:L.129, C:L.248, G:L.23, G:L.30, G:L.37 Hydrogen bonds: C:L.125, G:N.34 Salt bridges: G:H.38

5 x UNL: UNKNOWN LIGAND

UNL.19: 9 residues within 4Å: Chain C: V.89, T.93, F.96, W.238, H.241, F.242, V.245, V.246, F.249 9 PLIP interactions: 9 interactions with chain C Hydrophobic interactions: C:V.89, C:V.89, C:F.96, C:W.238, C:W.238, C:H.241, C:F.242, C:V.245, C:V.246 UNL.20: 5 residues within 4Å: Chain C: Q.159, I.163, T.166, Y.170 Ligands: CHD.18 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:I.163, C:T.166, C:Y.170, C:Y.170 UNL.21: 7 residues within 4Å: Chain A: L.110 Chain C: S.27, T.30, M.31, F.35 Chain J: S.46, C.49 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain A Hydrophobic interactions: C:T.30, C:F.35, A:L.110 UNL.33: 4 residues within 4Å: Chain C: I.43 Chain J: G.41, G.42, Y.45 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:I.43 UNL.35: 3 residues within 4Å: Chain L: T.25, L.26 Chain M: V.21 3 PLIP interactions: 2 interactions with chain L, 1 interactions with chain M Hydrophobic interactions: L:T.25, L:L.26, M:V.21

1 x PSC: (7R,17E,20E)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSA-17,20-DIEN-1-AMINIUM 4-OXIDE(Non-covalent)

PSC.24: 18 residues within 4Å: Chain A: F.321, H.328 Chain B: L.37, I.41, M.45, H.52, T.55, M.56, D.57, E.60, V.61, W.65, L.68 Chain E: H.1, E.2, T.3, D.4, F.7 12 PLIP interactions: 2 interactions with chain E, 9 interactions with chain B, 1 interactions with chain A Salt bridges: E:H.1, E:D.4, B:H.52 Hydrophobic interactions: B:L.37, B:I.41, B:D.57, B:V.61, B:W.65, B:W.65, B:W.65, B:L.68, A:F.321

1 x ZN: ZINC ION(Non-covalent)

ZN.26: 4 residues within 4Å: Chain F: C.60, C.62, C.82, C.85 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:C.60, F:C.62, F:C.82, F:C.85

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

DMU.36: 12 residues within 4Å: Chain A: L.35, F.459, L.462 Chain D: W.95 Chain M: L.27, L.28, A.30, G.31, W.32, L.34, Y.35, H.36 7 PLIP interactions: 2 interactions with chain D, 2 interactions with chain M, 3 interactions with chain A Hydrophobic interactions: D:W.95, D:W.95, M:A.30, A:L.35, A:F.459, A:L.462 Hydrogen bonds: M:Y.35

1 x HEC: HEME C(Covalent)

HEC.37: 23 residues within 4Å: Chain N: K.14, C.15, C.18, H.19, T.29, G.30, P.31, L.36, T.41, G.42, F.47, Y.49, T.50, N.53, W.60, Y.68, L.69, T.79, K.80, M.81, I.82, F.83, L.99 19 PLIP interactions: 19 interactions with chain N, Hydrophobic interactions: N:P.31, N:L.36, N:F.47, N:Y.49, N:Y.68, N:L.69, N:M.81, N:F.83, N:L.99 Hydrogen bonds: N:G.42, N:T.50, N:N.53, N:N.53, N:T.79, N:T.79, N:K.80 Salt bridges: N:K.80 pi-Stacking: N:Y.68 Metal complexes: N:H.19

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Shimada, S. et al., Complex structure of cytochrome c-cytochrome c oxidase reveals a novel protein-protein interaction mode. EMBO J. (2017)

Release Date

2017-01-11

Peptides

Cytochrome c oxidase subunit 1: A
Cytochrome c oxidase subunit 2: B
Cytochrome c oxidase subunit 3: C
Cytochrome c oxidase subunit 4 isoform 1, mitochondrial: D
Cytochrome c oxidase subunit 5A, mitochondrial: E
Cytochrome c oxidase subunit 5B, mitochondrial: F
Cytochrome c oxidase subunit 6A2, mitochondrial: G
Cytochrome c oxidase subunit 6B1: H
Cytochrome c oxidase subunit 6C: I
Cytochrome c oxidase subunit 7A1, mitochondrial: J
Cytochrome c oxidase subunit 7B, mitochondrial: K
Cytochrome c oxidase subunit 7C, mitochondrial: L
Cytochrome c oxidase subunit 8B, mitochondrial: M
Cytochrome c: N

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

I
I

J
J

K
K

L
L

M
M

N
1

Membrane

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

Cytochrome c oxidase subunit 2

Cytochrome c oxidase subunit 3

Cytochrome c oxidase subunit 4 isoform 1, mitochondrial

Cytochrome c oxidase subunit 5A, mitochondrial

Cytochrome c oxidase subunit 5B, mitochondrial

Cytochrome c oxidase subunit 6A2, mitochondrial

Cytochrome c oxidase subunit 6B1

Cytochrome c oxidase subunit 6C

Cytochrome c oxidase subunit 7A1, mitochondrial

Cytochrome c oxidase subunit 7B, mitochondrial

Cytochrome c oxidase subunit 7C, mitochondrial

Cytochrome c oxidase subunit 8B, mitochondrial

Cytochrome c

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