SMTL ID : 5z84.2 (1 other biounit)

The structure of azide-bound cytochrome c oxidase determined using the crystals exposed to 20 mM azide solution for 4 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

3 x CDL: CARDIOLIPIN(Non-covalent)

CDL.1: 14 residues within 4Å: Chain A: F.282, L.283, D.300, Y.304, S.307, I.311 Chain B: A.70, L.73, A.77, L.78, L.81, R.82, Y.85 Ligands: CHD.28 14 PLIP interactions: 8 interactions with chain B, 6 interactions with chain A Hydrophobic interactions: B:A.70, B:L.73, B:A.77, B:L.78, B:L.81, B:R.82, B:Y.85, A:F.282, A:L.283, A:Y.304, A:I.311, A:I.311 Hydrogen bonds: B:Y.85, A:D.300 CDL.31: 22 residues within 4Å: Chain C: M.51, L.52, M.54, Y.55, W.58, R.59, I.62, R.63, F.67, T.174, S.212, T.213, I.216, V.217, F.220, R.221, K.224, H.226 Chain J: K.8, F.12, L.31 Ligands: PGV.30 24 PLIP interactions: 21 interactions with chain C, 3 interactions with chain J Hydrophobic interactions: C:M.51, C:L.52, C:Y.55, C:Y.55, C:Y.55, C:W.58, C:W.58, C:R.59, C:I.62, C:T.174, C:T.213, C:I.216, C:I.216, C:V.217, C:F.220, J:L.31 Hydrogen bonds: C:R.59, C:R.63 Salt bridges: C:R.63, C:K.224, C:K.224, C:H.226, J:K.8 Water bridges: J:D.28 CDL.55: 16 residues within 4Å: Chain C: N.125, L.127, L.131, L.138, V.142 Chain G: L.23, A.24, S.27, L.30, C.31, N.34, L.37, H.38 Ligands: PEK.34, DMU.35, PEK.53 11 PLIP interactions: 7 interactions with chain G, 4 interactions with chain C Hydrophobic interactions: G:L.23, G:L.30, G:L.30, G:L.37, C:L.131, C:L.138, C:L.138 Hydrogen bonds: G:N.34, C:N.125 Salt bridges: G:H.38, G:H.38

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

HEA.2: 34 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, V.70, I.73, G.125, W.126, Y.371, V.374, F.377, H.378, L.381, S.382, V.386, F.393, T.424, F.425, Q.428, R.438, R.439, Y.440, S.458, V.465, M.468 37 PLIP interactions: 37 interactions with chain A, Hydrophobic interactions: A:A.24, A:T.31, A:I.37, A:R.38, A:V.58, A:V.58, A:A.62, A:M.65, A:I.66, A:V.70, A:I.73, A:V.374, A:F.377, A:F.377, A:L.381, A:F.393, A:F.393, A:T.424, A:F.425, A:V.465 Hydrogen bonds: A:R.38, A:Y.54, A:W.126, A:Y.371, 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:F.377, A:F.425 Metal complexes: A:H.61, A:H.378 HEA.3: 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.7, AZI.8 29 PLIP interactions: 25 interactions with chain A, 4 interactions with chain B, Hydrophobic interactions: A:W.236, A:V.243, A:V.243, A:I.247, A:T.309, A:T.316, A:V.320, A:F.348, A:L.353, A:V.373, A:F.377, A:F.377, A:V.380, A:L.381, A:L.381, B:I.34, B:I.34, B:P.69, B:I.72 Hydrogen bonds: A:W.126, A:Y.244 Water bridges: A:T.316, A:D.369, A:R.438, A:R.439 Salt bridges: A:H.368, A:R.438 pi-Stacking: A:H.290 Metal complexes: A:H.376

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

CU.4: 5 residues within 4Å: Chain A: H.240, H.290, H.291 Ligands: AZI.7, AZI.8 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.5: 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.9, H2O.11, H2O.13

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

NA.6: 5 residues within 4Å: Chain A: E.40, G.45, T.46, S.441, D.442 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.43 Water bridges: A:Q.43

2 x AZI: AZIDE ION(Non-covalent)

AZI.7: 9 residues within 4Å: Chain A: W.236, G.239, H.240, V.243, H.290, H.291 Ligands: HEA.3, CU.4, AZI.8 No protein-ligand interaction detected (PLIP) AZI.8: 7 residues within 4Å: Chain A: H.240, Y.244, H.290, T.309 Ligands: HEA.3, CU.4, AZI.7 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.244, A:H.290

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

PGV.9: 29 residues within 4Å: Chain A: F.94, P.95, R.96, M.97, F.148, L.152, 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, F.86, S.89, F.93 Ligands: PGV.30, PEK.54 19 PLIP interactions: 11 interactions with chain C, 8 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.86, C:F.93, A:F.148, A:L.152, A:V.155 Hydrogen bonds: A:R.96, A:R.96, A:M.97 Water bridges: A:A.93 Salt bridges: A:R.96 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.9, CDL.31 28 PLIP interactions: 26 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:I.62, C:F.86, C:I.210, C:I.210, C:T.213, C:F.214, 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: 17 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, H.10 Chain M: A.3, K.4, P.5, P.12, Q.15, A.16, L.19, S.20 16 PLIP interactions: 5 interactions with chain M, 5 interactions with chain A, 3 interactions with chain D, 3 interactions with chain K Hydrophobic interactions: M:P.12, M:P.12, M:A.16, M:L.19, A:T.408, A:W.409, A:I.412, D:T.80, D:F.87, D:F.87, K:F.9, K:F.9 Hydrogen bonds: M:A.3, A:T.408 Water bridges: A:R.480 Salt bridges: K:H.10

3 x TGL: TRISTEAROYLGLYCEROL(Non-covalent)

TGL.10: 18 residues within 4Å: Chain A: F.346, T.354, Y.379, F.418, 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 Ligands: TGL.41 14 PLIP interactions: 9 interactions with chain A, 3 interactions with chain B, 2 interactions with chain I Hydrophobic interactions: A:F.346, A:F.346, A:T.354, A:F.418, A:F.426, A:F.426, A:F.426, A:H.429, A:F.430, B:L.7, B:F.32 Salt bridges: B:H.24, I:R.43 Water bridges: I:R.43 TGL.41: 20 residues within 4Å: Chain A: W.334, L.342, G.343, F.414, A.415 Chain B: L.39, I.42, S.43, L.46, T.47, K.49 Chain D: R.73, S.74, T.75, E.77, W.78, V.81 Chain I: R.16, H.20 Ligands: TGL.10 15 PLIP interactions: 5 interactions with chain B, 4 interactions with chain D, 6 interactions with chain A Hydrophobic interactions: B:L.39, B:I.42, B:L.46, B:T.47, B:K.49, D:E.77, D:W.78, D:V.81, A:W.334, A:W.334, A:L.342, A:F.414, A:F.414 Hydrogen bonds: D:W.78 Salt bridges: A:K.411 TGL.60: 26 residues within 4Å: Chain A: F.2, T.17, L.18, L.20, L.21, F.22, W.25, P.106, L.110, L.113, F.393, F.400, S.401, I.472 Chain L: N.10, I.11, P.12, F.13, S.14, R.20, M.24, M.25, L.27, F.28, F.29 Ligands: EDO.11 21 PLIP interactions: 12 interactions with chain A, 9 interactions with chain L Hydrophobic interactions: A:L.18, A:L.20, A:L.21, A:L.21, A:F.22, A:W.25, A:W.25, A:W.25, A:W.25, A:L.113, A:F.400, A:I.472, L:I.11, L:F.13, L:F.13, L:L.27, L:F.28, L:F.28, L:F.28, L:F.29, L:F.29

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

EDO.11: 2 residues within 4Å: Chain A: F.2 Ligands: TGL.60 Ligand excluded by PLIP EDO.12: 8 residues within 4Å: Chain A: Y.19, M.71, P.72, G.76, S.101, L.105, S.156, S.157 Ligand excluded by PLIP EDO.13: 3 residues within 4Å: Chain A: P.131, D.221, P.222 Ligand excluded by PLIP EDO.14: 5 residues within 4Å: Chain A: Q.52, A.120, A.137, H.138, A.139 Ligand excluded by PLIP EDO.15: 6 residues within 4Å: Chain A: H.256, T.259, K.265, T.490, N.491 Ligands: EDO.51 Ligand excluded by PLIP EDO.16: 7 residues within 4Å: Chain A: Y.260, Y.261, V.394, H.395, P.398, W.494 Chain M: I.1 Ligand excluded by PLIP EDO.17: 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.18: 5 residues within 4Å: Chain A: N.496, F.505, E.507 Chain F: I.57, W.73 Ligand excluded by PLIP EDO.19: 6 residues within 4Å: Chain A: K.265, T.489 Chain F: I.70, P.83, S.84 Ligands: EDO.22 Ligand excluded by PLIP EDO.20: 7 residues within 4Å: Chain A: E.507 Chain C: T.5 Chain F: P.30, N.32, P.50, R.56, L.96 Ligand excluded by PLIP EDO.21: 9 residues within 4Å: Chain A: P.174, T.509, Y.510, V.511 Chain F: N.32, L.34, A.35, P.36, R.56 Ligand excluded by PLIP EDO.22: 5 residues within 4Å: Chain A: K.265 Chain F: N.66, T.68, S.84 Ligands: EDO.19 Ligand excluded by PLIP EDO.25: 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.26: 3 residues within 4Å: Chain B: T.125, L.135, F.206 Ligand excluded by PLIP EDO.27: 1 residues within 4Å: Chain B: 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: 4 residues within 4Å: Chain C: H.3, Q.4, H.70 Chain F: L.16 Ligand excluded by PLIP EDO.40: 5 residues within 4Å: Chain C: N.12, P.13 Chain J: G.17, L.18, P.19 Ligand excluded by PLIP EDO.42: 5 residues within 4Å: Chain D: D.26, V.27, A.28, K.63 Chain E: R.30 Ligand excluded by PLIP EDO.43: 2 residues within 4Å: Chain D: E.144, W.145 Ligand excluded by PLIP EDO.44: 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.45: 3 residues within 4Å: Chain E: R.14, W.15, Y.18 Ligand excluded by PLIP EDO.46: 5 residues within 4Å: Chain E: V.16, N.20, D.49, A.50, R.53 Ligand excluded by PLIP EDO.47: 3 residues within 4Å: Chain E: Y.18, K.21, E.28 Ligand excluded by PLIP EDO.48: 4 residues within 4Å: Chain E: D.23, I.24, D.25, L.58 Ligand excluded by PLIP EDO.49: 3 residues within 4Å: Chain E: R.53, R.56, R.57 Ligand excluded by PLIP EDO.51: 7 residues within 4Å: Chain A: T.489, T.490 Chain F: S.67, T.68, V.69, W.71 Ligands: EDO.15 Ligand excluded by PLIP EDO.52: 3 residues within 4Å: Chain F: F.72, Q.80, R.81 Ligand excluded by PLIP EDO.56: 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.57: 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.58: 5 residues within 4Å: Chain I: N.53, Y.54, D.55, D.59, E.62 Ligand excluded by PLIP

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

CUA.23: 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.24: 24 residues within 4Å: Chain A: F.268, F.321, L.324, A.325, H.328 Chain B: I.41, M.45, H.52, M.56, D.57, V.61, I.64, W.65, L.68, P.69, I.72 Chain E: E.6, T.7, D.8, F.11, L.41 Chain I: R.10, A.14, L.17 17 PLIP interactions: 4 interactions with chain A, 10 interactions with chain B, 1 interactions with chain I, 2 interactions with chain E Hydrophobic interactions: A:F.268, A:F.321, A:L.324, A:A.325, B:I.41, B:I.41, B:M.56, B:V.61, B:I.64, B:W.65, B:L.68, B:P.69, B:I.72, I:L.17 Hydrogen bonds: B:D.57 Salt bridges: E:D.8 pi-Cation interactions: E:F.11

3 x CHD: CHOLIC ACID(Non-covalent)

CHD.28: 8 residues within 4Å: Chain A: H.233, D.300, T.301, Y.304, F.305 Chain C: W.99, H.103 Ligands: CDL.1 8 PLIP interactions: 5 interactions with chain A, 3 interactions with chain C Hydrophobic interactions: A:Y.304, A:F.305, C:W.99 Hydrogen bonds: A:T.301, C:W.99 Water bridges: A:T.301 Salt bridges: A:H.233, C:H.103 CHD.32: 6 residues within 4Å: Chain C: R.156, Q.161, 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.59: 5 residues within 4Å: Chain A: I.3, F.8 Chain J: Y.32, R.33, T.37 3 PLIP interactions: 2 interactions with chain J, 1 interactions with chain A Hydrophobic interactions: J:R.33, J:R.33, A:I.3

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)

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

DMU.33: 10 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, W.52 Ligands: DMU.36 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain C Hydrophobic interactions: A:L.110, A:A.114, C:M.33, C:F.37 DMU.35: 6 residues within 4Å: Chain C: W.116, P.117, W.258, W.259, S.261 Ligands: CDL.55 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:W.258, C:W.258, C:W.258 Hydrogen bonds: C:W.116, C:W.259, 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: L.38, Y.45 Ligands: DMU.33 6 PLIP interactions: 5 interactions with chain C, 1 interactions with chain J Hydrogen bonds: C:N.38, C:N.38, C:S.39, C:S.39, C:S.39 Hydrophobic interactions: J:L.38 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 9 PLIP interactions: 4 interactions with chain D, 1 interactions with chain A, 4 interactions with chain M Hydrophobic interactions: D:L.95, D:W.98, D:W.98, A:L.35, M:L.27, M:L.27, M:L.34 Hydrogen bonds: D:Y.102 Water bridges: M:H.36

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.34: 14 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, W.36 Ligands: CDL.55 13 PLIP interactions: 4 interactions with chain G, 8 interactions with chain C, 1 interactions with chain F Hydrophobic interactions: G:L.23, C:I.165, C:L.169, C:Y.172, C:Y.172, C:Y.172 Hydrogen bonds: G:R.17, C:K.157, C:H.158, C:Q.161, F:A.1 Water bridges: G:R.17 Salt bridges: G:R.17 PEK.53: 6 residues within 4Å: Chain G: S.2, A.3, K.5, D.7, L.23 Ligands: CDL.55 3 PLIP interactions: 3 interactions with chain G Hydrophobic interactions: G:A.3, G:K.5, G:L.23 PEK.54: 25 residues within 4Å: Chain A: H.151, V.155, A.203, T.207, L.215 Chain C: L.31, W.34, A.178, Y.181, Y.182, A.184, F.186, T.187, I.188, F.198, G.202, F.203, I.209 Chain G: W.62, T.68, F.69, F.70, H.71, N.76 Ligands: PGV.9 17 PLIP interactions: 7 interactions with chain C, 3 interactions with chain A, 7 interactions with chain G Hydrophobic interactions: C:L.31, C:W.34, C:A.178, C:F.203, C:I.209, A:V.155, A:A.203, A:L.215, G:W.62, G:F.69 Hydrogen bonds: C:A.184, C:I.188, G:T.68, G:F.70, G:N.76, G:N.76 Water bridges: G:F.69

1 x ZN: ZINC ION(Non-covalent)

ZN.50: 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 11, 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 11, Cytochrome c oxidase subunit 7B, mitochondrial

Cytochrome c oxidase subunit 7C, mitochondrial

Cytochrome c oxidase subunit 8B, mitochondrial

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