SMTL ID : 5x19.1 (1 other biounit)

CO bound cytochrome c oxidase at 100 micro sec after pump laser irradiation to release CO from O2 reduction center

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: 30 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, I.66, M.69, V.70, I.73, G.125, W.126, Y.371, F.377, H.378, L.381, S.382, V.386, T.424, F.425, Q.428, R.438, R.439, Y.440, V.465, M.468 34 PLIP interactions: 34 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:I.66, A:V.70, A:F.377, A:L.381, A:L.381, A:V.386, A:T.424, A:F.425, A:F.425, A:F.425, A:V.465 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:R.438, A:R.438 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: 32 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, 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: CMO.6 27 PLIP interactions: 23 interactions with chain A, 4 interactions with chain B, Hydrophobic interactions: A:W.236, A:V.243, A:I.247, A:I.247, A:T.309, A:A.313, A:V.320, A:L.353, A:I.356, A:L.358, A:F.377, A:F.377, A:V.380, A:L.381, B:I.34, B:P.69, B:I.72, B:L.73 Hydrogen bonds: A:W.126, A:Y.244 Water bridges: A:H.291, A:D.369, A:D.369, A:R.439 Salt bridges: A:H.368, A:R.438 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 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.10

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

NA.5: 4 residues within 4Å: Chain A: E.40, G.45, S.441, D.442 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.441 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 TGL: TRISTEAROYLGLYCEROL(Non-covalent)

TGL.7: 17 residues within 4Å: Chain A: F.346, V.350, Y.379, N.422, F.426, H.429, F.430, L.433, W.450 Chain B: L.7, G.8, L.28, V.31, F.32, S.35, L.39 Chain I: R.43 13 PLIP interactions: 4 interactions with chain B, 8 interactions with chain A, 1 interactions with chain I Hydrophobic interactions: B:V.31, B:F.32, B:L.39, A:F.346, A:V.350, A:F.426, A:F.426, A:H.429, A:F.430, A:W.450, A:W.450 Salt bridges: B:H.24, I:R.43 TGL.30: 11 residues within 4Å: Chain A: W.334, G.343, F.414, A.415 Chain B: T.47 Chain D: S.74, T.75, E.77, W.78, V.81 Chain I: R.16 9 PLIP interactions: 4 interactions with chain D, 4 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: D:W.78, D:V.81, A:W.334, A:F.414, A:F.414, A:A.415, B:T.47 Hydrogen bonds: D:T.75, D:W.78 TGL.43: 19 residues within 4Å: Chain A: F.2, T.17, L.21, F.22, W.25, F.393, F.400, I.472 Chain L: N.10, I.11, P.12, F.13, S.14, R.20, M.24, M.25, F.28, F.29, S.31 10 PLIP interactions: 5 interactions with chain A, 5 interactions with chain L Hydrophobic interactions: A:F.22, A:W.25, A:W.25, A:F.393, A:I.472, L:I.11, L:F.13, L:F.28, L:F.28, L:F.29

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: 23 residues within 4Å: Chain A: F.94, P.95, R.96, M.97, P.200 Chain C: H.9, G.20, A.24, T.28, N.50, M.54, W.57, W.58, V.61, E.64, H.71, L.79, G.82, M.83, F.86, S.89, F.93 Ligands: PGV.20 12 PLIP interactions: 5 interactions with chain A, 7 interactions with chain C Hydrophobic interactions: A:P.200, C:A.24, C:W.57, C:W.57, C:W.57, C:F.86, C:F.86, C:F.93 Hydrogen bonds: A:R.96, A:R.96, A:M.97 Salt bridges: A:R.96 PGV.9: 17 residues within 4Å: Chain A: N.406, T.408, W.409, R.480 Chain D: T.80, A.84, F.87 Chain K: H.10, V.17, S.20 Chain M: A.3, K.4, P.5, T.10, P.12, Q.15, S.20 13 PLIP interactions: 2 interactions with chain K, 5 interactions with chain M, 2 interactions with chain D, 4 interactions with chain A Hydrophobic interactions: K:V.17, M:P.12, M:P.12, M:Q.15, D:A.84, D:F.87, A:W.409 Salt bridges: K:H.10 Hydrogen bonds: M:A.3, A:T.408 Water bridges: M:A.6, A:R.480, A:R.480 PGV.20: 22 residues within 4Å: Chain C: M.54, W.58, V.61, S.65, T.66, F.86, E.90, F.93, 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.21 24 PLIP interactions: 2 interactions with chain F, 22 interactions with chain C Water bridges: F:Q.12, F:E.17, C:S.65, C:R.221, C:H.231, C:H.231 Hydrophobic interactions: C:W.58, C:W.58, C:W.58, C:W.58, C:F.86, C:F.93, C:I.210, C:T.213, C:F.214, C:F.214, C:F.214 Hydrogen bonds: C:S.65, C:R.221, C:F.233, C:G.234 Salt bridges: C:R.221, C:R.221, C:H.231 PGV.25: 9 residues within 4Å: Chain C: T.95, W.99, Y.102, H.103, A.107 Chain H: N.22, N.24 Ligands: CHD.23, EDO.26 8 PLIP interactions: 5 interactions with chain C, 3 interactions with chain H Hydrophobic interactions: C:T.95, C:W.99, C:W.99 Water bridges: C:H.103, H:N.22, H:N.24 Salt bridges: C:H.103 Hydrogen bonds: H:N.22

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

EDO.10: 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.11: 2 residues within 4Å: Chain A: Y.304 Ligands: CHD.23 Ligand excluded by PLIP EDO.12: 8 residues within 4Å: Chain A: N.4, R.5, S.9, T.10, N.11, Y.502 Chain C: P.13 Chain L: Y.3 Ligand excluded by PLIP EDO.13: 5 residues within 4Å: Chain A: F.67, L.105, A.153, S.156, S.157 Ligand excluded by PLIP EDO.17: 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.18: 4 residues within 4Å: Chain A: L.136, A.137 Chain B: D.158, V.159 Ligand excluded by PLIP EDO.26: 2 residues within 4Å: Chain C: Y.102 Ligands: PGV.25 Ligand excluded by PLIP EDO.27: 3 residues within 4Å: Chain C: G.141, T.145 Ligands: CDL.35 Ligand excluded by PLIP EDO.28: 1 residues within 4Å: Chain C: F.251 Ligand excluded by PLIP EDO.29: 7 residues within 4Å: Chain C: W.146, S.150, D.155, H.158 Chain F: A.1 Chain G: A.13, R.14 Ligand excluded by PLIP EDO.32: 7 residues within 4Å: Chain A: Y.510 Chain F: P.36, K.37, T.39, P.46, N.47, L.48 Ligand excluded by PLIP EDO.33: 7 residues within 4Å: Chain A: Q.180, P.182, T.490 Chain F: S.67, T.68, V.69, W.71 Ligand excluded by PLIP EDO.38: 7 residues within 4Å: Chain C: G.120 Chain G: A.46, F.47, I.48, Y.50, L.53, R.54 Ligand excluded by PLIP EDO.39: 3 residues within 4Å: Chain C: E.111 Chain H: T.71, W.72 Ligand excluded by PLIP EDO.41: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP EDO.42: 1 residues within 4Å: Chain K: W.40 Ligand excluded by PLIP EDO.44: 1 residues within 4Å: Chain A: M.117 Ligand excluded by PLIP

1 x CUA: DINUCLEAR COPPER ION(Covalent)

CUA.14: 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

5 x CHD: CHOLIC ACID(Non-covalent)

CHD.15: 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.22: 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.23: 9 residues within 4Å: Chain A: H.233, W.288, D.300, T.301, Y.304 Chain C: W.99, H.103 Ligands: EDO.11, PGV.25 8 PLIP interactions: 4 interactions with chain C, 4 interactions with chain A Hydrophobic interactions: C:W.99, A:W.288, A:Y.304 Hydrogen bonds: C:W.99, A:T.301 Water bridges: C:H.103 Salt bridges: C:H.103, A:H.233 CHD.37: 6 residues within 4Å: Chain G: R.14, R.17, F.18, F.21, G.22 Ligands: PEK.24 5 PLIP interactions: 5 interactions with chain G Hydrophobic interactions: G:F.18 Water bridges: G:R.17, G:R.17 Salt bridges: G:R.14, G:R.17 CHD.40: 5 residues within 4Å: Chain J: Y.32, R.33, M.36, T.37, L.40 2 PLIP interactions: 2 interactions with chain J Hydrophobic interactions: J:R.33, J:L.40

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.16: 15 residues within 4Å: Chain A: F.321, A.325, H.328 Chain B: H.52, T.55, M.56, D.57, E.60, V.61, W.65, L.68 Chain E: D.8, F.11, L.41 Chain I: R.10 8 PLIP interactions: 4 interactions with chain B, 2 interactions with chain A, 2 interactions with chain E Hydrophobic interactions: B:M.56, B:V.61, B:W.65, B:L.68, A:F.321, A:A.325 Salt bridges: E:D.8 pi-Cation interactions: E:F.11

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

UNX.19: 4 residues within 4Å: Chain C: H.148, M.152, H.232, E.236 No protein-ligand interaction detected (PLIP)

2 x CDL: CARDIOLIPIN(Non-covalent)

CDL.21: 18 residues within 4Å: Chain C: T.48, M.51, L.52, Y.55, R.59, I.62, R.63, F.67, T.213, V.217, F.220, R.221, K.224, H.226 Chain J: K.8, T.27, L.31 Ligands: PGV.20 19 PLIP interactions: 16 interactions with chain C, 3 interactions with chain J Hydrophobic interactions: C:T.48, C:M.51, C:L.52, C:Y.55, C:R.59, C:I.62, C:T.213, C:V.217, J:L.31 Hydrogen bonds: C:Y.55, C:R.59 Salt bridges: C:R.63, C:K.224, C:K.224, C:K.224, C:K.224, C:H.226, J:K.8, J:K.8 CDL.35: 15 residues within 4Å: Chain C: N.125, L.131, T.134, S.135, V.142 Chain G: W.16, L.23, S.27, C.31, N.34, L.37, H.38 Ligands: PEK.24, EDO.27, PEK.36 12 PLIP interactions: 8 interactions with chain G, 4 interactions with chain C Hydrophobic interactions: G:W.16, G:L.23, G:L.23, G:N.34, G:L.37, C:L.131, C:T.134, C:V.142 Hydrogen bonds: G:N.34, G:H.38, C:N.125 Salt bridges: G:H.38

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.24: 12 residues within 4Å: Chain C: K.157, H.158, Q.161, T.168, Y.172 Chain F: A.1, G.3 Chain G: R.17, F.21, P.26 Ligands: CDL.35, CHD.37 9 PLIP interactions: 6 interactions with chain C, 3 interactions with chain G Hydrophobic interactions: C:T.168, C:Y.172, G:F.21, G:P.26 Water bridges: C:Q.161 Salt bridges: C:K.157, C:K.157, C:H.158, G:R.17 PEK.34: 21 residues within 4Å: Chain A: H.151, V.155, A.203, L.215 Chain C: W.34, Y.181, Y.182, A.184, F.186, T.187, I.188, F.198, G.202, G.205, L.206 Chain G: W.62, T.68, F.69, F.70, H.71, N.76 13 PLIP interactions: 3 interactions with chain A, 4 interactions with chain C, 6 interactions with chain G Hydrophobic interactions: A:V.155, A:A.203, A:L.215, C:W.34, C:Y.181, G:F.69 Hydrogen bonds: C:A.184, C:I.188, G:T.68, G:F.70, G:N.76 Water bridges: G:F.69, G:F.69 PEK.36: 6 residues within 4Å: Chain G: A.1, S.2, K.5, G.6, H.8 Ligands: CDL.35 1 PLIP interactions: 1 interactions with chain G Hydrophobic interactions: G:K.5

1 x ZN: ZINC ION(Non-covalent)

ZN.31: 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

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

DMU.45: 12 residues within 4Å: Chain A: L.35, F.459 Chain D: W.98, Y.102 Chain L: F.37 Chain M: L.27, L.28, G.31, W.32, L.34, Y.35, H.36 9 PLIP interactions: 3 interactions with chain M, 2 interactions with chain A, 1 interactions with chain L, 3 interactions with chain D Hydrophobic interactions: M:L.34, A:L.35, A:F.459, L:F.37, D:W.98, D:W.98, D:W.98 Hydrogen bonds: M:W.32 Water bridges: M:H.36

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
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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