SMTL ID : 5x1b.2 (1 other biounit)

CO bound cytochrome c oxidase at 20 nsec after pump laser irradiation to release CO from O2 reduction center

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 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: 25 residues within 4Å: Chain A: M.28, T.31, S.34, I.37, R.38, Y.54, V.58, H.61, A.62, M.65, V.70, I.73, G.125, W.126, Y.371, F.377, H.378, S.382, V.386, F.425, Q.428, R.438, R.439, Y.440, M.468 29 PLIP interactions: 29 interactions with chain A, Hydrophobic interactions: A:T.31, A:I.37, A:V.58, A:V.58, A:A.62, A:M.65, A:V.70, A:I.73, A:F.377, A:V.386 Hydrogen bonds: A:S.34, A:S.34, A:R.38, A:Y.54, A:W.126, A:Y.371, A:Q.428, A:R.439, A:Y.440 Water bridges: A:T.127, 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: 29 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, 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 Ligands: CMO.6 28 PLIP interactions: 26 interactions with chain A, 2 interactions with chain B, Hydrophobic interactions: A:W.126, A:W.236, A:V.243, A:V.243, A:T.309, A:A.313, A:T.316, A:V.320, A:L.353, A:L.358, A:F.377, A:F.377, A:V.380, A:L.381, A:L.381, B:I.34, B:I.34 Hydrogen bonds: A:W.126, A:Y.244 Water bridges: A:T.316, A:D.369, A:D.369, A:R.438, A:R.438 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: 4 residues within 4Å: Chain A: H.240, H.290, H.291 Ligands: CMO.6 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:H.240, A:H.290, A:H.291, CMO.6

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 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:H.368, A:D.369, H2O.3, H2O.6, H2O.7

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:E.40 Water bridges: A:Q.43

1 x CMO: CARBON MONOXIDE(Non-functional Binders)

CMO.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)

3 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: A.84, F.87 Chain K: F.9 Chain M: P.12, Q.15, A.16 10 PLIP interactions: 4 interactions with chain A, 3 interactions with chain D, 2 interactions with chain M, 1 interactions with chain K Hydrophobic interactions: A:W.409, A:W.409, D:A.84, D:F.87, D:F.87, M:P.12, M:A.16, K:F.9 Hydrogen bonds: A:N.406, A:T.408 PGV.8: 18 residues within 4Å: Chain A: F.94, P.95, R.96, M.97 Chain C: H.9, A.24, M.27, N.50, M.54, W.57, W.58, V.61, E.64, H.71, L.79, F.93 Ligands: PEK.16, PGV.17 10 PLIP interactions: 6 interactions with chain C, 4 interactions with chain A Hydrophobic interactions: C:A.24, C:M.27, C:W.57, C:W.57, C:F.93 Hydrogen bonds: C:H.71, A:R.96, A:R.96, A:M.97 Salt bridges: A:R.96 PGV.17: 21 residues within 4Å: Chain C: M.54, W.58, V.61, S.65, T.66, F.86, L.206, H.207, I.210, T.213, F.214, R.221, H.226, F.227, H.231, H.232, F.233, G.234 Ligands: PGV.8, PEK.16, CDL.18 25 PLIP interactions: 24 interactions with chain C, 1 interactions with chain F Hydrophobic interactions: C:W.58, C:W.58, C:W.58, C:W.58, C:W.58, C:F.86, C:L.206, C:I.210, C:I.210, C:T.213, C:F.214, C:F.214, C:F.214, C:F.233 Hydrogen bonds: C:S.65, C:R.221, C:F.233, C:G.234 Water bridges: C:R.221, C:H.231, C:H.231, F:E.17 Salt bridges: C:R.221, C:R.221, C:H.231

3 x TGL: TRISTEAROYLGLYCEROL(Non-covalent)

TGL.9: 12 residues within 4Å: Chain A: V.350, N.422, F.426, H.429, F.430, L.433 Chain B: L.7, G.8, H.24, L.28, F.32, S.35 9 PLIP interactions: 5 interactions with chain A, 3 interactions with chain B, 1 interactions with chain I Hydrophobic interactions: A:V.350, A:F.426, A:F.426, A:F.430, A:F.430, B:L.7, B:L.7, B:F.32 Salt bridges: I:R.43 TGL.10: 13 residues within 4Å: Chain A: W.334, M.339, K.411 Chain B: L.39, I.42, S.43, L.46, T.47 Chain D: S.74, E.77, V.81, M.86 Chain I: R.16 7 PLIP interactions: 4 interactions with chain B, 2 interactions with chain A, 1 interactions with chain D Hydrophobic interactions: B:L.39, B:I.42, B:L.46, B:T.47, A:W.334, D:V.81 Salt bridges: A:K.411 TGL.11: 20 residues within 4Å: Chain A: F.2, I.3, T.17, L.20, L.21, F.22, W.25, W.81, F.397, F.400, I.472, F.476 Chain L: P.12, F.13, S.14, M.24, M.25, F.28, F.29, S.31 16 PLIP interactions: 11 interactions with chain A, 5 interactions with chain L Hydrophobic interactions: A:F.2, A:I.3, A:T.17, A:L.20, A:F.22, A:W.25, A:W.25, A:F.397, A:F.400, A:I.472, A:F.476, L:F.13, L:F.13, L:F.13, L:F.28, L:F.29

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

EDO.12: 6 residues within 4Å: Chain A: Y.260, Y.261, H.395, P.398, W.494 Chain M: I.1 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.260, A:Y.260, A:V.394, A:H.395 EDO.26: 4 residues within 4Å: Chain G: K.5, F.18, L.19, L.23 1 PLIP interactions: 1 interactions with chain G Hydrogen bonds: G:K.5

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

CUA.13: 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

4 x CHD: CHOLIC ACID(Non-covalent)

CHD.14: 7 residues within 4Å: Chain A: M.271, G.272, W.275 Chain B: Q.59, E.62, T.63, T.66 6 PLIP interactions: 3 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:M.271, A:W.275, A:W.275 Hydrogen bonds: B:Q.59, B:E.62, B:T.63 CHD.19: 7 residues within 4Å: Chain C: R.156, L.160, Q.161, F.164, F.219, L.223 Chain J: F.1 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:L.160, C:F.164, C:F.164, C:F.219, C:L.223 Salt bridges: C:R.156 CHD.20: 6 residues within 4Å: Chain A: H.233, D.300, T.301, Y.304 Chain C: W.99, H.103 6 PLIP interactions: 2 interactions with chain C, 4 interactions with chain A Hydrogen bonds: C:W.99, A:T.301 Salt bridges: C:H.103, A:H.233 Hydrophobic interactions: A:Y.304 Water bridges: A:T.301 CHD.27: 5 residues within 4Å: Chain J: Y.32, R.33, M.36, T.37, L.40 5 PLIP interactions: 5 interactions with chain J Hydrophobic interactions: J:Y.32, J:R.33, J:L.40 Hydrogen bonds: J:R.33, J:R.33

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

UNX.15: 3 residues within 4Å: Chain C: H.148, H.232, E.236 No protein-ligand interaction detected (PLIP)

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.16: 22 residues within 4Å: Chain A: H.151, V.155, L.210, L.215 Chain C: Y.181, Y.182, A.184, F.186, T.187, I.188, F.198, G.202, L.206 Chain G: W.62, T.68, F.69, F.70, H.71, N.76 Ligands: PGV.8, PGV.17, CDL.18 11 PLIP interactions: 3 interactions with chain A, 6 interactions with chain G, 2 interactions with chain C Hydrophobic interactions: A:V.155, A:L.210, A:L.215, G:F.69 Hydrogen bonds: G:F.70, G:F.70, G:N.76, C:Y.181, C:I.188 Water bridges: G:F.69, G:F.69 PEK.23: 5 residues within 4Å: Chain G: S.2, A.3, K.5, H.8 Ligands: CDL.25 2 PLIP interactions: 2 interactions with chain G Hydrophobic interactions: G:K.5, G:K.5 PEK.24: 7 residues within 4Å: Chain C: K.157, H.158, T.168 Chain G: R.17, F.21, L.23 Ligands: CDL.25 7 PLIP interactions: 3 interactions with chain C, 4 interactions with chain G Hydrophobic interactions: C:T.168, G:L.23 Hydrogen bonds: C:K.157, C:K.157, G:R.17 Salt bridges: G:R.17, G:R.17

2 x CDL: CARDIOLIPIN(Non-covalent)

CDL.18: 12 residues within 4Å: Chain C: M.51, L.52, Y.55, R.59, I.62, R.63, F.67, K.224, H.226 Chain J: K.8 Ligands: PEK.16, PGV.17 9 PLIP interactions: 8 interactions with chain C, 1 interactions with chain J Hydrophobic interactions: C:L.52, C:I.62 Hydrogen bonds: C:Y.55 Salt bridges: C:R.63, C:K.224, C:K.224, C:K.224, C:H.226, J:K.8 CDL.25: 12 residues within 4Å: Chain C: N.125, L.127, L.131, W.258 Chain G: L.23, S.27, C.31, N.34, L.37, H.38 Ligands: PEK.23, PEK.24 7 PLIP interactions: 4 interactions with chain G, 3 interactions with chain C Hydrophobic interactions: G:L.23, G:L.37, C:L.131, C:W.258 Hydrogen bonds: G:N.34, C:N.125 Salt bridges: G:H.38

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.21: 11 residues within 4Å: Chain A: H.328 Chain B: H.52, T.55, D.57, E.60, V.61, W.65 Chain E: Y.39, D.40, L.41 Chain I: A.14 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain I Hydrophobic interactions: B:D.57, B:V.61, B:W.65, B:W.65, I:A.14 Salt bridges: B:H.52

1 x ZN: ZINC ION(Non-covalent)

ZN.22: 5 residues within 4Å: Chain F: C.60, C.62, C.82, C.85, T.87 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.28: 9 residues within 4Å: Chain D: W.98, Y.102 Chain L: F.37 Chain M: L.27, L.28, A.30, G.31, W.32, Y.35 7 PLIP interactions: 3 interactions with chain D, 1 interactions with chain L, 3 interactions with chain M Hydrophobic interactions: D:W.98, D:W.98, L:F.37, M:L.27, M:A.30 Hydrogen bonds: D:Y.102, M:Y.35

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Shimada, A. et al., A nanosecond time-resolved XFEL analysis of structural changes associated with CO release from cytochrome c oxidase. Sci Adv (2017)

Release Date

2017-08-09

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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