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

azide-bound cytochrome c oxidase structure determined using the crystals exposed to 2 mM azide solution for 2 days

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 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: 37 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, V.374, F.377, H.378, L.381, S.382, V.386, M.390, F.393, M.417, T.424, F.425, Q.428, R.438, R.439, Y.440, S.458, V.465, M.468 36 PLIP interactions: 36 interactions with chain A, Hydrophobic interactions: A:A.24, 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:L.381, A:V.386, A:V.386, A:F.393, A:T.424, 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.425 Metal complexes: A:H.61, A:H.378 HEA.2: 35 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.321, 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 37 PLIP interactions: 33 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:T.316, A:V.320, A:F.321, A:F.348, A:F.348, A:T.349, A:I.356, 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:I.34, B:P.69, B:I.72 Hydrogen bonds: A:W.126, A:Y.244 Water bridges: A:H.291, 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 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: 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.11, H2O.11, H2O.14

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

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

2 x AZI: AZIDE ION(Non-covalent)

AZI.6: 7 residues within 4Å: Chain A: H.240, Y.244, H.290, T.309 Ligands: HEA.2, CU.3, AZI.7 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.244, A:H.290 AZI.7: 7 residues within 4Å: Chain A: H.240, V.243, H.290, H.291 Ligands: HEA.2, CU.3, AZI.6 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.8: 30 residues within 4Å: Chain A: F.94, P.95, R.96, M.97, F.148, I.158, L.159, P.200 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, E.90 Ligands: PGV.30, PEK.49 16 PLIP interactions: 8 interactions with chain A, 8 interactions with chain C Hydrophobic interactions: A:F.148, A:I.158, A:L.159, A:P.200, C:A.24, C:T.28, C:L.31, C:T.53, C:W.57, C:W.57, C:W.57, C:W.58 Hydrogen bonds: A:R.96, A:M.97 Water bridges: A:A.93 Salt bridges: A:R.96 PGV.9: 13 residues within 4Å: Chain A: N.406, T.408, W.409, I.412 Chain D: A.84, F.87 Chain K: F.9, H.10 Chain M: P.12, Q.15, A.16, L.19, S.20 15 PLIP interactions: 4 interactions with chain K, 3 interactions with chain M, 3 interactions with chain D, 5 interactions with chain A Hydrophobic interactions: K:F.9, K:F.9, K:F.9, M:Q.15, M:A.16, M:L.19, D:A.84, D:F.87, D:F.87, A:T.408, A:W.409, A:W.409, A:W.409 Salt bridges: K:H.10 Hydrogen bonds: A:T.408 PGV.30: 27 residues within 4Å: Chain C: M.51, M.54, W.58, V.61, I.62, S.65, T.66, H.71, M.83, F.86, E.90, L.206, H.207, 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: PGV.8, CDL.31 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:F.86, C:L.206, C:I.209, C:I.210, 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.34: 12 residues within 4Å: Chain A: D.298 Chain C: T.95, W.99, H.103, L.106, A.107 Chain H: F.20, N.22, N.24, R.27 Ligands: EDO.14, CHD.27 10 PLIP interactions: 5 interactions with chain C, 4 interactions with chain H, 1 interactions with chain A Hydrophobic interactions: C:T.95, C:W.99, C:W.99, C:W.99 Salt bridges: C:H.103 Hydrogen bonds: H:N.22, H:N.24, A:D.298 Water bridges: H:N.24, H:N.24

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

EDO.10: 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.11: 5 residues within 4Å: Chain A: Q.52, A.120, A.137, H.138, A.139 Ligand excluded by PLIP EDO.12: 3 residues within 4Å: Chain A: L.136, A.137 Chain B: Q.103 Ligand excluded by PLIP EDO.13: 6 residues within 4Å: Chain A: H.256, T.259, K.265, T.490, N.491 Ligands: EDO.46 Ligand excluded by PLIP EDO.14: 4 residues within 4Å: Chain A: W.288, Y.304 Ligands: CHD.27, PGV.34 Ligand excluded by PLIP EDO.15: 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.16: 5 residues within 4Å: Chain A: K.265, T.489 Chain F: I.70, P.83, S.84 Ligand excluded by PLIP EDO.17: 7 residues within 4Å: Chain A: K.265, E.266 Chain B: T.55 Chain F: N.66, T.68, I.70, S.84 Ligand excluded by PLIP EDO.18: 5 residues within 4Å: Chain A: Y.261, K.333, S.335, D.407 Chain M: I.1 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.23: 5 residues within 4Å: Chain A: P.222 Chain B: P.176, G.177 Chain C: E.111 Ligands: EDO.24 Ligand excluded by PLIP EDO.24: 2 residues within 4Å: Chain B: E.157 Ligands: EDO.23 Ligand excluded by PLIP EDO.25: 3 residues within 4Å: Chain B: H.102, E.157, D.158 Ligand excluded by PLIP EDO.26: 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.39: 8 residues within 4Å: Chain A: R.38, A.39, G.42, S.455, F.459 Chain D: L.96, E.99, Y.104 Ligand excluded by PLIP EDO.40: 2 residues within 4Å: Chain D: L.94, I.97 Ligand excluded by PLIP EDO.42: 4 residues within 4Å: Chain E: Y.18, K.21, I.24, E.28 Ligand excluded by PLIP EDO.43: 3 residues within 4Å: Chain E: R.53, R.56, R.57 Ligand excluded by PLIP EDO.44: 6 residues within 4Å: Chain D: K.56 Chain E: L.93, N.94, G.97, I.98, S.99 Ligand excluded by PLIP EDO.46: 7 residues within 4Å: Chain A: T.489, T.490 Chain F: S.67, T.68, V.69, W.71 Ligands: EDO.13 Ligand excluded by PLIP EDO.47: 6 residues within 4Å: Chain A: Y.510 Chain F: P.36, K.37, T.39, N.47, L.48 Ligand excluded by PLIP EDO.48: 3 residues within 4Å: Chain C: H.231 Chain F: D.9, E.17 Ligand excluded by PLIP EDO.52: 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.53: 4 residues within 4Å: Chain C: F.35 Chain G: K.58, P.59, S.61 Ligand excluded by PLIP EDO.56: 3 residues within 4Å: Chain C: P.13 Chain L: H.2, Y.3 Ligand excluded by PLIP EDO.58: 3 residues within 4Å: Chain M: S.20, F.23, L.24 Ligand excluded by PLIP

3 x TGL: TRISTEAROYLGLYCEROL(Non-covalent)

TGL.20: 17 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, L.28, V.31, F.32, S.35, S.36, L.39 Chain I: R.43 16 PLIP interactions: 5 interactions with chain B, 9 interactions with chain A, 2 interactions with chain I Hydrophobic interactions: B:L.7, B:V.31, B:F.32, B:L.39, A:F.346, A:F.346, A:V.350, A:F.426, A:F.426, A:F.426, A:F.426, A:H.429, A:F.430 Salt bridges: B:H.24, I:R.43 Water bridges: I:R.43 TGL.38: 22 residues within 4Å: Chain A: W.334, M.339, L.342, G.343, F.414, A.415, F.418, V.419 Chain B: L.39, I.42, S.43, T.47, K.49 Chain D: R.73, S.74, T.75, E.77, W.78, V.81, M.86 Chain I: R.16, H.20 16 PLIP interactions: 5 interactions with chain D, 9 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: D:V.81, A:W.334, A:W.334, A:W.334, A:L.342, A:F.414, A:A.415, A:F.418, A:V.419, B:L.39, B:T.47 Hydrogen bonds: D:T.75, D:W.78 Water bridges: D:T.75, D:T.75 Salt bridges: A:K.411 TGL.55: 20 residues within 4Å: Chain A: F.2, T.17, F.22, W.25, F.102, P.106, 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, F.28, F.29 19 PLIP interactions: 11 interactions with chain A, 8 interactions with chain L Hydrophobic interactions: A:F.2, A:F.2, A:F.2, A:W.25, A:W.25, A:W.25, A:F.102, A:L.113, A:F.393, A:F.400, A:I.472, L:I.11, L:F.13, L:F.13, L:F.13, L:F.28, L:F.28, L:F.29, L:F.29

5 x CHD: CHOLIC ACID(Non-covalent)

CHD.21: 7 residues within 4Å: Chain A: M.271, G.272, W.275 Chain B: Q.59, E.62, T.63, T.66 7 PLIP interactions: 4 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:M.271, A:W.275, A:W.275, A:W.275 Hydrogen bonds: B:Q.59, B:E.62, B:T.63 CHD.27: 9 residues within 4Å: Chain A: H.233, W.288, D.300, T.301, Y.304 Chain C: W.99, H.103 Ligands: EDO.14, PGV.34 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: 6 residues within 4Å: Chain C: R.156, L.160, 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:L.160, C:F.164, C:F.164, C:F.219, C:L.223 Salt bridges: C:R.156 Hydrogen bonds: J:F.1 CHD.50: 6 residues within 4Å: Chain G: R.14, R.17, F.18, F.21, G.22 Ligands: PEK.33 7 PLIP interactions: 7 interactions with chain G Hydrophobic interactions: G:F.18, G:F.18, G:F.21 Water bridges: G:R.17, G:R.17 Salt bridges: G:R.14, G:R.17 CHD.54: 8 residues within 4Å: Chain A: I.3, L.7, F.8 Chain J: Y.32, R.33, M.36, T.37, L.40 6 PLIP interactions: 5 interactions with chain J, 1 interactions with chain A Hydrophobic interactions: J:Y.32, J:R.33, J:M.36, A:I.3 Hydrogen bonds: J:Y.32, J:Y.32

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

CUA.22: 6 residues within 4Å: Chain B: H.161, C.196, E.198, C.200, H.204, M.207 8 PLIP interactions: 7 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.161, B:C.196, B:C.196, B:E.198, B:C.200, B:C.200, B:H.204, H2O.10

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

DMU.28: 11 residues within 4Å: Chain C: S.29, T.32, M.33, F.37 Chain J: Y.45, S.46, Y.48, C.49, L.50, W.52 Ligands: DMU.37 8 PLIP interactions: 5 interactions with chain C, 3 interactions with chain J Hydrophobic interactions: C:T.32, C:M.33, C:F.37, C:F.37, J:L.50 Water bridges: C:F.37 Hydrogen bonds: J:Y.45, J:Y.45 DMU.36: 5 residues within 4Å: Chain C: W.116, P.117, W.258, W.259, S.261 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:W.258 Hydrogen bonds: C:W.116, C:W.259, C:S.261 Water bridges: C:S.261 DMU.37: 10 residues within 4Å: Chain C: M.33, N.38, S.39, T.41, I.45 Chain J: T.37, G.41, G.42, Y.45 Ligands: DMU.28 12 PLIP interactions: 7 interactions with chain C, 5 interactions with chain J Hydrophobic interactions: C:I.45, J:T.37, J:Y.45, J:Y.45 Hydrogen bonds: C:N.38, C:N.38, C:N.38, C:S.39, C:T.41, J:Y.45, J:Y.45 Water bridges: C:F.37 DMU.57: 13 residues within 4Å: Chain A: F.459, L.462 Chain D: W.98, Y.102 Chain L: F.37 Chain M: L.27, L.28, A.30, G.31, W.32, L.34, Y.35, H.36 10 PLIP interactions: 3 interactions with chain A, 2 interactions with chain D, 4 interactions with chain M, 1 interactions with chain L Hydrophobic interactions: A:F.459, A:F.459, A:L.462, D:W.98, D:W.98, M:L.27, M:A.30, M:L.34, L:F.37 Water bridges: M:H.36

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

UNX.29: 4 residues within 4Å: Chain C: H.148, M.152, H.232, E.236 No protein-ligand interaction detected (PLIP)

1 x CDL: CARDIOLIPIN(Non-covalent)

CDL.31: 26 residues within 4Å: Chain C: T.48, M.51, L.52, M.54, Y.55, W.58, R.59, I.62, R.63, F.67, V.171, T.174, I.209, S.212, T.213, I.216, V.217, F.220, R.221, K.224, H.226 Chain J: K.8, F.12, T.27, L.31 Ligands: PGV.30 25 PLIP interactions: 20 interactions with chain C, 5 interactions with chain J Hydrophobic interactions: C:T.48, C:M.51, C:M.54, C:Y.55, C:W.58, C:W.58, C:R.59, C:I.62, C:V.171, C:T.174, C:I.209, C:T.213, C:I.216, C:F.220, J:L.31 Hydrogen bonds: C:Y.55, C:R.59 Salt bridges: C:R.63, C:K.224, C:K.224, C:H.226, J:K.8, J:K.8, J:K.8 Water bridges: J:D.28

4 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.33: 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, P.26 Ligands: CHD.50 13 PLIP interactions: 7 interactions with chain C, 6 interactions with chain G Hydrophobic interactions: C:I.165, C:L.169, C:Y.172, C:Y.172, G:F.21, G:F.21, G:L.23 Hydrogen bonds: C:K.157, C:H.158, C:Q.161, G:R.17 Salt bridges: G:R.17, G:R.17 PEK.35: 12 residues within 4Å: Chain C: Y.81, I.84, V.91, F.94, T.95, F.98, E.236, W.240, F.244, V.247, V.248, F.251 14 PLIP interactions: 14 interactions with chain C Hydrophobic interactions: C:Y.81, C:I.84, C:V.91, C:F.94, C:F.98, C:F.98, C:F.98, C:W.240, C:W.240, C:W.240, C:V.247, C:V.248, C:F.251 Hydrogen bonds: C:W.240 PEK.49: 24 residues within 4Å: Chain A: H.151, V.155, A.203, T.207, L.210, L.215 Chain C: W.34, 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 17 PLIP interactions: 7 interactions with chain G, 6 interactions with chain C, 4 interactions with chain A Hydrophobic interactions: G:F.69, C:W.34, C:I.188, C:F.203, C:F.203, A:V.155, A:L.210, A:L.215, A:L.215 Hydrogen bonds: G:T.68, G:F.70, G:N.76, G:N.76, C:A.184, C:I.188 Water bridges: G:F.69, G:F.69 PEK.51: 4 residues within 4Å: Chain G: S.2, D.7, T.11, L.19 1 PLIP interactions: 1 interactions with chain G Hydrophobic interactions: G:L.19

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.41: 19 residues within 4Å: Chain A: F.321, 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 Chain E: H.5, E.6, D.40 Chain I: L.13, A.14, L.17 14 PLIP interactions: 9 interactions with chain B, 2 interactions with chain A, 3 interactions with chain I Hydrophobic interactions: B:I.41, B:M.56, B:D.57, B:I.64, B:W.65, B:L.68, B:P.69, A:F.321, A:A.325, I:L.13, I:A.14 Salt bridges: B:H.52, B:H.52 Hydrogen bonds: I:A.14

1 x ZN: ZINC ION(Non-covalent)

ZN.45: 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
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

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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