SMTL ID : 5z86.2 (1 other biounit)

azide-bound cytochrome c oxidase structure determined using the crystals exposed to 20 mM azide solution for 3 days

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.85 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: 35 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, I.73, G.125, W.126, Y.371, F.377, H.378, L.381, S.382, V.386, M.390, F.393, T.424, F.425, Q.428, R.438, R.439, Y.440, S.458, V.465, M.468 32 PLIP interactions: 32 interactions with chain A, Hydrophobic interactions: A:A.24, A:T.31, A:I.37, A:V.58, A:V.58, A:A.62, A:M.65, A:I.66, A:V.70, A:F.377, A:L.381, A:L.381, A:F.393, A:T.424, A:F.425, A:F.425 Hydrogen bonds: A:R.38, A:Y.54, A:W.126, A:Y.371, 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:F.377, A:F.425 Metal complexes: A:H.61, A:H.378 HEA.2: 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 Ligands: AZI.6, AZI.7 38 PLIP interactions: 4 interactions with chain B, 34 interactions with chain A, Hydrophobic interactions: B:I.34, B:I.34, B:P.69, B:I.72, A:W.236, 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:V.320, A:F.348, A:F.348, A:L.353, A:L.358, A:L.358, A:V.373, A:F.377, A:F.377, A:V.380, A:L.381, A:L.381 Hydrogen bonds: A:W.126, A:Y.244 Water bridges: A:Y.244, A:H.291, A:D.369, A:D.369, A:R.438, A:R.439 Salt bridges: A:H.368, A:R.438, A:R.439 pi-Stacking: A:H.290 Metal complexes: A:H.376

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

CU.3: 5 residues within 4Å: Chain A: H.240, H.290, H.291 Ligands: AZI.6, AZI.7 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: 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.8, H2O.9, H2O.9

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

NA.5: 3 residues within 4Å: Chain A: E.40, G.45, S.441 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.40 Water bridges: A:Q.43

2 x AZI: AZIDE ION(Non-covalent)

AZI.6: 9 residues within 4Å: Chain A: W.236, G.239, H.240, V.243, H.290, H.291 Ligands: HEA.2, CU.3, AZI.7 No protein-ligand interaction detected (PLIP) AZI.7: 7 residues within 4Å: Chain A: H.240, Y.244, H.290, T.309 Ligands: HEA.2, CU.3, AZI.6 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.244, A:H.290

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

PGV.8: 31 residues within 4Å: Chain A: F.94, P.95, R.96, M.97, M.100, F.148, V.155 Chain C: H.9, V.11, G.20, A.24, M.27, T.28, L.31, N.50, T.53, M.54, W.57, W.58, V.61, E.64, H.71, L.79, G.82, M.83, F.86, S.89, E.90, F.93 Ligands: PGV.30, PEK.53 16 PLIP interactions: 10 interactions with chain C, 6 interactions with chain A Hydrophobic interactions: C:A.24, C:T.28, C:L.31, C:T.53, C:W.57, C:W.57, C:W.57, C:W.58, C:F.86, C:F.93, A:F.148 Hydrogen bonds: A:R.96, A:R.96, A:M.97 Water bridges: A:A.93 Salt bridges: A:R.96 PGV.28: 9 residues within 4Å: Chain A: D.298 Chain C: T.95, W.99, Y.102, H.103, A.107 Chain H: N.22, N.24 Ligands: CHD.26 7 PLIP interactions: 4 interactions with chain C, 3 interactions with chain H Hydrophobic interactions: C:T.95, C:W.99, C:W.99 Salt bridges: C:H.103 Hydrogen bonds: H:N.22 Water bridges: H:N.24, H:N.24 PGV.30: 23 residues within 4Å: Chain C: M.54, W.58, V.61, I.62, S.65, T.66, H.71, L.79, F.86, H.207, I.210, T.213, F.214, R.221, H.226, F.227, T.228, H.231, H.232, F.233, G.234 Ligands: PGV.8, CDL.31 29 PLIP interactions: 27 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:F.86, 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:R.221, C:F.233, C:G.234 Water bridges: C:S.65, C:R.221, C:H.231, C:H.231, F:Q.12, F:E.17 Salt bridges: C:R.221, C:R.221, C:H.231 PGV.61: 13 residues within 4Å: Chain A: N.406, T.408, W.409, I.412 Chain D: T.80, A.84, F.87 Chain K: F.9 Chain M: P.12, Q.15, A.16, L.19, S.20 14 PLIP interactions: 5 interactions with chain D, 2 interactions with chain M, 4 interactions with chain A, 3 interactions with chain K Hydrophobic interactions: D:T.80, D:F.87, D:F.87, D:F.87, D:F.87, M:P.12, M:A.16, A:W.409, A:W.409, A:I.412, K:F.9, K:F.9, K:F.9 Hydrogen bonds: A:T.408

3 x TGL: TRISTEAROYLGLYCEROL(Non-covalent)

TGL.9: 16 residues within 4Å: Chain A: F.346, V.350, Y.379, N.422, F.426, H.429, F.430, L.433 Chain B: L.7, G.8, H.24, L.28, F.32, S.35, L.39 Chain I: R.43 16 PLIP interactions: 12 interactions with chain A, 2 interactions with chain B, 2 interactions with chain I Hydrophobic interactions: A:F.346, A:V.350, A:Y.379, A:N.422, A:F.426, A:F.426, A:F.426, A:F.426, A:F.426, A:H.429, A:F.430, A:F.430, B:L.7 Salt bridges: B:H.24, I:R.43 Water bridges: I:R.43 TGL.40: 18 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.73, S.74, T.75, E.77, W.78 Chain I: R.16, H.20 13 PLIP interactions: 4 interactions with chain D, 7 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: D:W.78, A:W.334, A:W.334, A:W.334, A:L.342, A:F.414, A:F.414, B:L.39, B:L.46 Hydrogen bonds: D:T.75, D:E.77, D:W.78 Salt bridges: A:K.411 TGL.60: 22 residues within 4Å: Chain A: F.2, T.17, L.21, F.22, W.25, P.106, L.110, L.113, F.393, F.400, S.401, I.472 Chain L: I.11, P.12, F.13, S.14, R.20, M.24, M.25, F.28, F.29 Ligands: EDO.10 17 PLIP interactions: 9 interactions with chain L, 8 interactions with chain A Hydrophobic interactions: L:I.11, L:F.13, L:F.13, L:F.13, L:F.28, L:F.28, L:F.28, L:F.29, L:F.29, A:T.17, A:L.21, A:W.25, A:W.25, A:W.25, A:L.113, A:F.400, A:I.472

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

EDO.10: 2 residues within 4Å: Chain A: F.2 Ligands: TGL.60 Ligand excluded by PLIP EDO.11: 9 residues within 4Å: Chain A: Y.19, M.71, P.72, I.75, G.76, S.101, L.105, S.156, S.157 Ligand excluded by PLIP EDO.12: 2 residues within 4Å: Chain A: P.131, D.221 Ligand excluded by PLIP EDO.13: 4 residues within 4Å: Chain A: Q.52, A.137, H.138, A.139 Ligand excluded by PLIP EDO.14: 6 residues within 4Å: Chain A: H.256, T.259, K.265, T.490, N.491 Ligands: EDO.50 Ligand excluded by PLIP EDO.15: 6 residues within 4Å: Chain A: Y.260, Y.261, V.394, H.395, W.494 Chain M: I.1 Ligand excluded by PLIP EDO.16: 8 residues within 4Å: Chain A: L.483, T.484, V.485, T.488, W.494, G.497, C.498 Chain D: Y.11 Ligand excluded by PLIP EDO.17: 6 residues within 4Å: Chain A: N.496, T.504, F.505, E.506, E.507 Chain F: W.73 Ligand excluded by PLIP EDO.18: 5 residues within 4Å: Chain A: K.265, T.489 Chain F: I.70, P.83, S.84 Ligand excluded by PLIP EDO.19: 6 residues within 4Å: Chain A: E.507 Chain C: T.5 Chain F: P.30, N.32, P.50, R.56 Ligand excluded by PLIP EDO.20: 9 residues within 4Å: Chain A: R.5, N.11, K.13, D.14, W.81, P.499, P.500, Y.502 Chain L: N.10 Ligand excluded by PLIP EDO.23: 7 residues within 4Å: Chain A: Y.447 Chain B: M.1, A.2, Q.10, L.136, P.166, Y.193 Ligand excluded by PLIP EDO.24: 3 residues within 4Å: Chain B: T.125, L.135, F.206 Ligand excluded by PLIP EDO.25: 2 residues within 4Å: Chain B: T.63, I.67 Ligand excluded by PLIP EDO.37: 9 residues within 4Å: Chain C: W.146, S.150, D.155, H.158 Chain F: A.1, S.2 Chain G: A.13, R.14, R.17 Ligand excluded by PLIP EDO.38: 4 residues within 4Å: Chain A: P.222, A.223 Chain B: G.177 Chain C: E.111 Ligand excluded by PLIP EDO.39: 3 residues within 4Å: Chain C: H.3, H.70 Chain F: L.16 Ligand excluded by PLIP EDO.41: 5 residues within 4Å: Chain D: D.26, V.27, A.28, K.63 Chain E: R.30 Ligand excluded by PLIP EDO.42: 6 residues within 4Å: Chain D: Y.22, D.26 Chain E: W.27, R.30, K.31, N.34 Ligand excluded by PLIP EDO.43: 2 residues within 4Å: Chain D: E.144, W.145 Ligand excluded by PLIP EDO.44: 3 residues within 4Å: Chain E: R.14, W.15, Y.18 Ligand excluded by PLIP EDO.45: 5 residues within 4Å: Chain E: V.16, N.20, D.49, A.50, R.53 Ligand excluded by PLIP EDO.46: 3 residues within 4Å: Chain E: Y.18, K.21, E.28 Ligand excluded by PLIP EDO.47: 3 residues within 4Å: Chain E: D.23, D.25, L.58 Ligand excluded by PLIP EDO.48: 3 residues within 4Å: Chain E: R.53, R.56, R.57 Ligand excluded by PLIP EDO.50: 7 residues within 4Å: Chain A: T.489, T.490 Chain F: S.67, T.68, V.69, W.71 Ligands: EDO.14 Ligand excluded by PLIP EDO.51: 3 residues within 4Å: Chain F: F.72, Q.80, R.81 Ligand excluded by PLIP EDO.52: 8 residues within 4Å: Chain A: P.174, T.509, Y.510, V.511 Chain F: N.32, L.34, P.36, R.56 Ligand excluded by PLIP EDO.55: 6 residues within 4Å: Chain C: G.120 Chain G: A.46, F.47, I.48, L.53, R.54 Ligand excluded by PLIP EDO.56: 6 residues within 4Å: Chain C: T.119 Chain G: Y.50 Chain H: F.81, P.82, G.83, K.84 Ligand excluded by PLIP EDO.57: 5 residues within 4Å: Chain I: N.53, Y.54, D.55, D.59, E.62 Ligand excluded by PLIP EDO.59: 5 residues within 4Å: Chain C: N.12, P.13 Chain J: G.17, L.18, P.19 Ligand excluded by PLIP

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

CUA.21: 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.22: 24 residues within 4Å: Chain A: F.268, F.321, L.324, A.325, H.328 Chain B: I.41, M.45, H.52, T.55, M.56, D.57, E.60, V.61, I.64, W.65, L.68, P.69, I.72 Chain E: E.6, D.8, F.11, L.41 Chain I: R.10, L.17 15 PLIP interactions: 9 interactions with chain B, 4 interactions with chain A, 1 interactions with chain E, 1 interactions with chain I Hydrophobic interactions: B:I.41, B:I.41, B:D.57, B:E.60, B:I.64, B:L.68, B:P.69, B:I.72, A:F.268, A:F.321, A:L.324, A:A.325, I:L.17 Hydrogen bonds: B:D.57 Salt bridges: E:D.8

3 x CHD: CHOLIC ACID(Non-covalent)

CHD.26: 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.28 8 PLIP interactions: 3 interactions with chain C, 5 interactions with chain A Hydrophobic interactions: C:W.99, A:W.288, A:Y.304 Hydrogen bonds: C:W.99, A:T.301 Salt bridges: C:H.103, A:H.233 Water bridges: A:T.301 CHD.32: 5 residues within 4Å: Chain C: R.156, F.164, F.219, L.223 Chain J: F.1 7 PLIP interactions: 6 interactions with chain C, 1 interactions with chain J Hydrophobic interactions: C:F.164, C:F.164, C:F.164, C:F.219, C:L.223 Salt bridges: C:R.156 Hydrogen bonds: J:F.1 CHD.58: 6 residues within 4Å: Chain A: I.3 Chain J: Y.32, R.33, M.36, T.37, L.40 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:I.3

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.27: 8 residues within 4Å: Chain C: I.84, V.91, T.95, F.98, W.240, F.244, V.247, F.251 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:V.91, C:V.91, C:F.98, C:W.240, C:F.251, C:F.251 PEK.34: 13 residues within 4Å: Chain C: K.157, H.158, Q.161, I.165, T.168, L.169, Y.172 Chain F: A.1 Chain G: R.17, F.21, G.22, L.23 Ligands: CDL.54 13 PLIP interactions: 8 interactions with chain C, 5 interactions with chain G Hydrophobic interactions: C:I.165, C:L.169, C:Y.172, C:Y.172, G:F.21, G:L.23 Hydrogen bonds: C:K.157, C:K.157, G:R.17 Water bridges: C:Q.161, C:Q.161 Salt bridges: G:R.17, G:R.17 PEK.53: 26 residues within 4Å: Chain A: H.151, V.155, A.203, T.207, L.210, L.215 Chain C: W.34, F.35, A.178, Y.181, Y.182, A.184, F.186, T.187, I.188, F.198, G.202, F.203, G.205 Chain G: W.62, T.68, F.69, F.70, H.71, N.76 Ligands: PGV.8 15 PLIP interactions: 4 interactions with chain C, 8 interactions with chain G, 3 interactions with chain A Hydrophobic interactions: C:W.34, C:F.35, C:F.203, G:W.62, G:F.69, A:V.155, A:A.203, A:L.210 Hydrogen bonds: C:I.188, G:T.68, G:F.70, G:N.76, G:N.76 Water bridges: G:F.69, G:F.69

1 x UNX: UNKNOWN ATOM OR ION(Non-functional Binders)

UNX.29: 3 residues within 4Å: Chain C: H.148, H.232, E.236 No protein-ligand interaction detected (PLIP)

2 x CDL: CARDIOLIPIN(Non-covalent)

CDL.31: 19 residues within 4Å: Chain C: M.51, L.52, M.54, Y.55, W.58, R.59, I.62, R.63, F.67, T.213, I.216, V.217, F.220, R.221, K.224, H.226 Chain J: K.8, F.12 Ligands: PGV.30 17 PLIP interactions: 16 interactions with chain C, 1 interactions with chain J Hydrophobic interactions: C:Y.55, C:W.58, C:W.58, C:R.59, C:I.62, C:T.213, C:I.216, C:V.217, C:F.220, C:F.220 Hydrogen bonds: C:Y.55 Water bridges: C:Y.55, J:D.28 Salt bridges: C:R.63, C:K.224, C:K.224, C:H.226 CDL.54: 15 residues within 4Å: Chain C: N.125, L.127, L.131, T.134, L.138, V.142, Y.253 Chain G: L.23, S.27, L.30, C.31, N.34, L.37, H.38 Ligands: PEK.34 13 PLIP interactions: 6 interactions with chain C, 7 interactions with chain G Hydrophobic interactions: C:L.131, C:T.134, C:L.138, C:L.138, C:Y.253, G:L.23, G:L.30, G:L.30, G:L.37 Hydrogen bonds: C:N.125, G:N.34 Salt bridges: G:H.38, G:H.38

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

DMU.33: 11 residues within 4Å: Chain A: L.110 Chain C: S.29, T.32, M.33, F.37 Chain J: S.46, Y.48, C.49, W.52, A.53 Ligands: DMU.36 5 PLIP interactions: 3 interactions with chain C, 1 interactions with chain J, 1 interactions with chain A Hydrophobic interactions: C:T.32, C:M.33, C:F.37, J:A.53, A:L.110 DMU.35: 6 residues within 4Å: Chain C: W.116, P.117, V.254, W.258, W.259, S.261 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:W.258, C:W.258 Hydrogen bonds: C:W.116, C:S.261 Water bridges: C:S.261 DMU.36: 7 residues within 4Å: Chain C: N.38, S.39, T.41, I.45 Chain J: G.42, Y.45 Ligands: DMU.33 8 PLIP interactions: 2 interactions with chain J, 6 interactions with chain C Hydrophobic interactions: J:Y.45, C:I.45 Hydrogen bonds: J:Y.45, C:N.38, C:N.38, C:S.39, C:S.39, C:S.39 DMU.62: 12 residues within 4Å: Chain A: L.35, F.459 Chain D: L.95, W.98, Y.102 Chain M: L.27, L.28, G.31, W.32, L.34, Y.35, H.36 7 PLIP interactions: 3 interactions with chain M, 3 interactions with chain D, 1 interactions with chain A Hydrophobic interactions: M:L.27, M:L.27, M:L.34, D:L.95, D:W.98, D:W.98, A:L.35

1 x ZN: ZINC ION(Non-covalent)

ZN.49: 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

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Shimada, A. et al., X-ray structural analyses of azide-bound cytochromecoxidases reveal that the H-pathway is critically important for the proton-pumping activity. J. Biol. Chem. (2018)

Release Date

2018-08-15

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

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 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

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