SMTL ID : 7xma.2 (1 other biounit)

Crystal structure of Bovine heart cytochrome c oxidase, apo structure with DMSO

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

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

Ligands

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

HEA.1: 36 residues within 4Å: Chain A: A.24, G.27, M.28, T.31, S.34, I.37, R.38, Y.54, V.58, H.61, A.62, M.65, I.66, M.69, V.70, G.125, W.126, Y.371, F.377, H.378, L.381, S.382, V.386, I.389, M.390, F.393, M.417, T.424, 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:V.58, A:V.58, A:A.62, A:M.65, A:I.66, A:V.70, A:F.377, A:F.377, A:L.381, A:I.389, A:F.393, A:F.393, A:T.424, A:F.425, 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 Salt bridges: A:R.438, A:R.439 pi-Stacking: A:H.61, A:H.378, A:F.425 Metal complexes: A:H.61, A:H.378 HEA.2: 33 residues within 4Å: Chain A: W.126, W.236, V.243, Y.244, 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 35 PLIP interactions: 30 interactions with chain A, 5 interactions with chain B, Hydrophobic interactions: A:W.236, A:V.243, A:T.309, A:V.320, A:F.348, A:I.356, A:I.356, A:L.358, A:L.358, 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: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:H.291, A:D.369, A:R.438, A:R.438, A:R.438 Salt bridges: A:H.368, A:R.438, A:R.439 pi-Stacking: A:H.376 pi-Cation interactions: A:H.240 Metal complexes: A:H.376

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

CU.3: 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.4: 4 residues within 4Å: Chain A: H.368, D.369 Chain B: S.197, E.198 6 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: A:H.368, A:D.369, B:E.198, H2O.13, H2O.13, H2O.16

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

NA.5: 3 residues within 4Å: Chain A: E.40, G.45, S.441 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.40, A:S.441 Water bridges: A:Q.43

1 x PER: PEROXIDE ION(Non-covalent)

PER.6: 6 residues within 4Å: Chain A: H.240, V.243, H.290, H.291 Ligands: HEA.2, CU.3 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: 24 residues within 4Å: Chain A: F.94, P.95, R.96, M.97, M.100, F.148, L.152 Chain C: H.9, A.24, T.28, N.50, M.54, W.57, W.58, V.61, E.64, H.71, G.82, M.83, F.86, S.89, E.90, F.93 Ligands: PEK.22 14 PLIP interactions: 8 interactions with chain C, 6 interactions with chain A Hydrophobic interactions: C:A.24, C:W.57, C:W.57, C:W.58, C:F.93, A:F.148, A:L.152 Hydrogen bonds: C:H.9, C:W.57, C:E.64, A:R.96, A:M.97 Water bridges: A:A.93 Salt bridges: A:R.96 PGV.9: 16 residues within 4Å: Chain A: N.406, T.408, W.409, I.412, R.480 Chain D: T.80, A.84, F.87 Chain K: F.9, H.10 Chain M: P.5, P.12, Q.15, A.16, L.19, S.20 14 PLIP interactions: 4 interactions with chain A, 5 interactions with chain D, 3 interactions with chain M, 2 interactions with chain K Hydrophobic interactions: A:T.408, A:W.409, A:I.412, D:T.80, D:A.84, D:F.87, D:F.87, D:F.87, M:P.12, M:A.16, K:F.9 Water bridges: A:T.404, M:A.3 Salt bridges: K:H.10 PGV.13: 12 residues within 4Å: Chain A: F.237, W.288, D.298 Chain C: T.95, W.99, Y.102, H.103, L.106, A.107 Chain H: N.22, N.24 Ligands: CHD.17 12 PLIP interactions: 5 interactions with chain C, 3 interactions with chain A, 4 interactions with chain H Hydrophobic interactions: C:T.95, C:W.99, C:W.99, C:L.106, A:F.237, A:W.288 Salt bridges: C:H.103 Water bridges: A:T.301, H:N.24, H:N.24 Hydrogen bonds: H:N.22, H:N.24 PGV.14: 24 residues within 4Å: Chain C: M.54, W.58, V.61, I.62, S.65, T.66, H.71, L.79, F.86, E.90, L.206, I.209, I.210, T.213, F.214, R.221, H.226, F.227, T.228, H.231, H.232, F.233, G.234 Ligands: CDL.15 32 PLIP interactions: 30 interactions with chain C, 2 interactions with chain F Hydrophobic interactions: C:W.58, C:W.58, C:W.58, C:W.58, C:W.58, C:W.58, C:I.62, C:F.86, C:L.206, C:I.209, C:I.210, C:I.210, C:T.213, C:F.214, C:F.214, C:F.214, C:F.214 Hydrogen bonds: C:S.65, C:S.65, C:T.66, C:H.71, C:R.221, C:F.233, C:G.234 Water bridges: C:S.65, C:R.221, C:H.231, F:Q.12, F:E.17 Salt bridges: C:R.221, C:R.221, C:H.231

3 x TGL: TRISTEAROYLGLYCEROL(Non-covalent)

TGL.8: 16 residues within 4Å: Chain A: V.350, Y.379, N.422, F.426, H.429, F.430, L.433 Chain B: L.7, G.8, H.24, L.28, V.31, F.32, S.35, S.36, L.39 19 PLIP interactions: 9 interactions with chain A, 9 interactions with chain B, 1 interactions with chain I Hydrophobic interactions: A:V.350, A:Y.379, A:F.426, A:F.426, A:F.426, A:F.426, A:H.429, A:F.430, A:F.430, B:L.28, B:V.31, B:F.32, B:F.32, B:F.32, B:L.39 Water bridges: B:G.8, B:F.9 Salt bridges: B:H.24, I:R.43 TGL.19: 18 residues within 4Å: Chain A: W.334, M.339, K.411, F.414, V.419 Chain B: L.39, I.42, S.43, T.47 Chain D: R.73, T.75, E.77, W.78, V.81, M.86, I.89 Chain I: R.16, H.20 9 PLIP interactions: 5 interactions with chain A, 2 interactions with chain D, 2 interactions with chain B Hydrophobic interactions: A:W.334, A:W.334, A:K.411, A:V.419, D:V.81, D:I.89, B:I.42, B:T.47 Salt bridges: A:K.411 TGL.25: 22 residues within 4Å: Chain A: F.2, T.17, L.18, L.20, L.21, F.22, W.25, F.102, P.106, F.109, L.113, F.400, I.472 Chain L: N.10, I.11, P.12, F.13, S.14, R.20, M.25, F.28, F.29 19 PLIP interactions: 12 interactions with chain A, 7 interactions with chain L Hydrophobic interactions: A:T.17, A:L.18, A:L.20, A:F.22, A:W.25, A:W.25, A:W.25, A:W.25, A:F.102, A:F.109, A:F.400, A:I.472, L:I.11, L:F.13, L:F.13, L:F.28, L:F.28, L:F.29, L:F.29

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

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.11: 18 residues within 4Å: Chain A: F.321, L.324, A.325, H.328 Chain B: L.37, I.41, M.45, H.52, M.56, D.57, V.61, W.65, L.68 Chain E: E.6, D.8, F.11 Chain I: R.10, L.17 15 PLIP interactions: 9 interactions with chain B, 5 interactions with chain A, 1 interactions with chain E Hydrophobic interactions: B:L.37, B:I.41, B:I.41, B:M.56, B:D.57, B:W.65, B:L.68, A:F.321, A:F.321, A:F.321, A:L.324, A:H.328 Water bridges: B:H.52, B:D.57 Salt bridges: E:D.8

3 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.12: 13 residues within 4Å: Chain A: V.193 Chain C: K.77, R.80, Y.81, I.84, L.85, I.88, V.91, T.95, W.240, F.244, V.247, F.251 12 PLIP interactions: 11 interactions with chain C, 1 interactions with chain A Hydrophobic interactions: C:I.84, C:I.84, C:L.85, C:I.88, C:V.91, C:W.240, C:F.244, C:V.247, A:V.193 Hydrogen bonds: C:K.77, C:K.77 Salt bridges: C:K.77 PEK.18: 11 residues within 4Å: Chain C: K.157, H.158, T.168, Y.172 Chain G: R.17, F.21, G.22, L.25, P.26 Ligands: CHD.21, CDL.23 10 PLIP interactions: 5 interactions with chain G, 5 interactions with chain C Hydrophobic interactions: G:L.25, G:P.26, C:Y.172, C:Y.172, C:Y.172 Hydrogen bonds: G:R.17, C:K.157, C:K.157 Water bridges: G:R.17 Salt bridges: G:R.17 PEK.22: 26 residues within 4Å: Chain A: H.151, V.155, A.203, T.207, L.210, L.215 Chain C: W.34, F.35, Y.181, Y.182, A.184, F.186, T.187, I.188, F.198, V.199, G.202, F.203, G.205 Chain G: W.62, T.68, F.69, F.70, H.71, N.76 Ligands: PGV.7 18 PLIP interactions: 8 interactions with chain C, 4 interactions with chain A, 6 interactions with chain G Hydrophobic interactions: C:W.34, C:F.35, C:Y.181, C:I.188, C:F.203, C:F.203, A:V.155, A:A.203, A:T.207, A:L.210, G:F.69, G:F.70 Hydrogen bonds: C:Y.181, C:I.188, G:T.68, G:F.70 Water bridges: G:F.69, G:F.69

2 x CDL: CARDIOLIPIN(Non-covalent)

CDL.15: 20 residues within 4Å: Chain C: M.51, L.52, Y.55, W.58, R.59, I.62, R.63, F.67, I.209, T.213, I.216, V.217, F.220, R.221, K.224, H.226 Chain J: K.8, F.12, L.31 Ligands: PGV.14 20 PLIP interactions: 17 interactions with chain C, 3 interactions with chain J Hydrophobic interactions: C:Y.55, C:Y.55, C:Y.55, C:W.58, C:W.58, C:R.59, C:I.209, C:T.213, C:F.220, J:L.31 Water bridges: C:Y.55, C:R.63, C:R.63 Salt bridges: C:R.63, C:K.224, C:K.224, C:K.224, C:H.226, J:K.8, J:K.8 CDL.23: 16 residues within 4Å: Chain C: L.127, L.131, S.135, L.138, V.142, L.250, Y.253, V.254 Chain G: L.23, S.27, L.30, C.31, N.34, L.37, H.38 Ligands: PEK.18 16 PLIP interactions: 11 interactions with chain G, 5 interactions with chain C Hydrophobic interactions: G:L.23, G:L.30, G:L.30, G:L.30, G:N.34, G:L.37, G:L.37, C:L.131, C:L.138, C:L.250, C:Y.253, C:V.254 Hydrogen bonds: G:N.34, G:H.38 Salt bridges: G:H.38, G:H.38

3 x CHD: CHOLIC ACID(Non-covalent)

CHD.16: 6 residues within 4Å: Chain C: R.156, L.160, Q.161, F.164, L.223 Chain J: F.1 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:L.160, C:L.160, C:F.164, C:F.164, C:L.223 Salt bridges: C:R.156 CHD.17: 9 residues within 4Å: Chain A: H.233, W.288, D.300, T.301, Y.304, F.305 Chain C: W.99, H.103 Ligands: PGV.13 12 PLIP interactions: 10 interactions with chain A, 2 interactions with chain C Hydrophobic interactions: A:W.288, A:T.301, A:Y.304, A:F.305 Hydrogen bonds: A:T.301, C:W.99 Water bridges: A:D.300, A:D.300, A:T.301, A:T.301 Salt bridges: A:H.233, C:H.103 CHD.21: 6 residues within 4Å: Chain G: R.14, R.17, F.18, F.21, G.22 Ligands: PEK.18 8 PLIP interactions: 8 interactions with chain G Hydrophobic interactions: G:F.18, G:F.18, G:F.21 Water bridges: G:R.17, G:R.17, G:R.17 Salt bridges: G:R.14, G:R.17

1 x ZN: ZINC ION(Non-covalent)

ZN.20: 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

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

DMU.24: 11 residues within 4Å: Chain A: L.110, A.114 Chain C: S.29, M.33, F.37 Chain J: S.46, Y.48, C.49, L.50, W.52, A.53 9 PLIP interactions: 4 interactions with chain C, 2 interactions with chain A, 3 interactions with chain J Hydrophobic interactions: C:M.33, C:F.37, C:F.37, A:L.110, A:A.114, J:L.50, J:A.53 Hydrogen bonds: C:F.37, J:Y.45 DMU.26: 14 residues within 4Å: Chain A: L.35, F.459, L.462 Chain D: L.95, W.98, Y.102 Chain L: F.37 Chain M: L.27, L.28, A.30, G.31, W.32, Y.35, H.36 13 PLIP interactions: 5 interactions with chain M, 3 interactions with chain A, 4 interactions with chain D, 1 interactions with chain L Hydrophobic interactions: M:L.27, M:L.27, M:A.30, A:L.35, A:F.459, A:L.462, D:L.95, D:W.98, D:W.98, D:W.98, L:F.37 Hydrogen bonds: M:W.32, M:Y.35

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nishida, Y. et al., Identifying antibiotics based on structural differences in the conserved allostery from mitochondrial heme-copper oxidases. Nat Commun (2022)

Release Date

2022-12-21

Peptides

Cytochrome c oxidase subunit 1: A
Cytochrome c oxidase subunit 2,Cytochrome c oxidase subunit 1: B
Cytochrome c oxidase subunit 3: C
Cytochrome c oxidase subunit 4 isoform 1: D
Cytochrome c oxidase subunit 5A: 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: J
Cytochrome c oxidase subunit 7B: K
Cytochrome c oxidase subunit 7C, mitochondrial: L
Cytochrome c oxidase subunit 8B: M

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
N

B
O

C
P

D
Q

E
R

F
S

G
T

H
U

I
V

J
W

K
X

L
Y

M
Z

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 1

Cytochrome c oxidase subunit 3

Cytochrome c oxidase subunit 4 isoform 1

Cytochrome c oxidase subunit 5A

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

Cytochrome c oxidase subunit 7B

Cytochrome c oxidase subunit 7C, mitochondrial

Cytochrome c oxidase subunit 8B

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