SMTL ID : 5x19.2 (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: 32 residues within 4Å: Chain A: A.24, 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, V.421, F.425, Q.428, R.438, R.439, Y.440, V.465 34 PLIP interactions: 34 interactions with chain A, Hydrophobic interactions: A:A.24, A:T.31, 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:V.386, A:F.393, A:V.421, 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: 29 residues within 4Å: Chain A: W.126, W.236, V.243, Y.244, I.247, H.290, H.291, T.309, 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 Ligands: CMO.6 30 PLIP interactions: 28 interactions with chain A, 2 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:I.356, 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:P.69 Hydrogen bonds: A:W.126, A:Y.244 Water bridges: A:H.291, A:T.316, A:D.369, A:D.369, A:R.438, A:R.438 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 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.5, H2O.8, H2O.10

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

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

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)

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

PGV.7: 14 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, S.20 Chain M: P.12, Q.15, A.16, L.19, S.20 13 PLIP interactions: 3 interactions with chain M, 3 interactions with chain D, 4 interactions with chain A, 3 interactions with chain K Hydrophobic interactions: M:P.12, M:P.12, M:L.19, D:A.84, D:F.87, D:F.87, A:W.409, A:I.412, K:F.9 Hydrogen bonds: A:N.406, A:T.408 Water bridges: K:F.9 Salt bridges: K:H.10 PGV.8: 23 residues within 4Å: Chain A: F.94, P.95, R.96, M.97, M.100, V.155 Chain C: H.9, V.11, A.24, M.27, N.50, M.54, W.57, W.58, V.61, E.64, H.71, L.79, G.82, F.86, S.89, E.90 Ligands: PGV.17 10 PLIP interactions: 5 interactions with chain A, 5 interactions with chain C Hydrophobic interactions: A:V.155, C:A.24, C:W.57, C:W.57, C:W.57, C:F.86 Hydrogen bonds: A:R.96, A:R.96, A:M.97 Salt bridges: A:R.96 PGV.15: 9 residues within 4Å: Chain A: D.298 Chain C: T.95, W.99, Y.102, H.103 Chain H: N.22, N.24 Ligands: EDO.9, CHD.20 5 PLIP interactions: 2 interactions with chain A, 2 interactions with chain H, 1 interactions with chain C Water bridges: A:D.298, A:D.298, H:N.22 Hydrogen bonds: H:N.22 Hydrophobic interactions: C:W.99 PGV.17: 20 residues within 4Å: Chain C: M.51, W.58, V.61, S.65, T.66, H.71, F.86, H.207, I.210, F.214, R.221, H.226, F.227, T.228, H.231, H.232, F.233, G.234 Ligands: PGV.8, CDL.18 20 PLIP interactions: 19 interactions with chain C, 1 interactions with chain F Hydrophobic interactions: C:W.58, C:W.58, C:W.58, C:F.86, C:I.210, C:I.210, C:I.210, 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:E.17 Salt bridges: C:R.221, C:R.221, C:H.231

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

EDO.9: 3 residues within 4Å: Chain A: W.288, Y.304 Ligands: PGV.15 No protein-ligand interaction detected (PLIP) EDO.10: 6 residues within 4Å: Chain A: T.484, V.485, D.486 Chain D: V.17 Chain M: I.1, T.2 3 PLIP interactions: 1 interactions with chain D, 1 interactions with chain M, 1 interactions with chain A Hydrogen bonds: D:Y.16, M:I.1 Water bridges: A:D.486 EDO.14: 7 residues within 4Å: Chain A: Y.447 Chain B: M.1, A.2, Q.10, L.136, P.166, Y.193 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:A.2, B:Q.10, B:Y.193, A:Y.447 Water bridges: B:A.2, B:Q.195 EDO.21: 3 residues within 4Å: Chain C: T.145, H.148, H.149 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:H.148 EDO.22: 3 residues within 4Å: Chain C: G.141, T.145, H.243 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:G.141 EDO.29: 4 residues within 4Å: Chain G: K.5, F.18, G.22, L.23 1 PLIP interactions: 1 interactions with chain G Hydrogen bonds: G:K.5

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

CUA.11: 6 residues within 4Å: Chain B: H.161, C.196, E.198, C.200, H.204, M.207 9 PLIP interactions: 7 interactions with chain B, 2 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.7, H2O.7

3 x TGL: TRISTEAROYLGLYCEROL(Non-covalent)

TGL.12: 14 residues within 4Å: Chain A: F.346, 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 Chain I: R.43 7 PLIP interactions: 1 interactions with chain B, 5 interactions with chain A, 1 interactions with chain I Hydrophobic interactions: B:F.32, A:F.346, A:V.350, A:F.426, A:F.426, A:F.426 Salt bridges: I:R.43 TGL.23: 16 residues within 4Å: Chain A: W.334, L.342, G.343, K.411 Chain B: I.42, S.43, T.47, K.49 Chain D: S.74, T.75, E.77, W.78, V.81, M.86 Chain I: R.16, H.20 9 PLIP interactions: 4 interactions with chain A, 4 interactions with chain D, 1 interactions with chain B Hydrophobic interactions: A:W.334, A:W.334, A:L.342, A:K.411, D:E.77, D:W.78, D:V.81, B:I.42 Hydrogen bonds: D:W.78 TGL.31: 17 residues within 4Å: Chain A: F.2, T.17, L.21, W.81, F.400, S.401, I.472 Chain L: N.10, I.11, P.12, F.13, S.14, M.24, M.25, F.28, F.29, S.31 12 PLIP interactions: 5 interactions with chain A, 7 interactions with chain L Hydrophobic interactions: A:T.17, A:L.21, A:W.81, A:F.400, A:I.472, L:I.11, L:F.13, L:F.13, L:F.28, L:F.28, L:F.29, L:F.29

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.13: 19 residues within 4Å: Chain A: F.321, L.324, A.325, H.328 Chain B: I.41, H.52, T.55, M.56, D.57, E.60, V.61, W.65, P.69, I.72 Chain E: D.8, F.11, L.41 Chain I: R.10, A.14 13 PLIP interactions: 1 interactions with chain I, 3 interactions with chain A, 7 interactions with chain B, 2 interactions with chain E Hydrophobic interactions: I:A.14, A:F.321, A:L.324, A:A.325, B:I.41, B:V.61, B:W.65, B:P.69, B:I.72 Hydrogen bonds: B:D.57 Salt bridges: B:H.52, E:D.8 pi-Cation interactions: E:F.11

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

UNX.16: 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.18: 15 residues within 4Å: Chain C: T.48, M.51, Y.55, W.58, I.62, R.63, F.67, T.213, V.217, F.220, K.224, H.226 Chain J: K.8, F.12 Ligands: PGV.17 16 PLIP interactions: 15 interactions with chain C, 1 interactions with chain J Hydrophobic interactions: C:T.48, C:M.51, C:Y.55, C:Y.55, C:Y.55, C:W.58, C:W.58, C:I.62, C:T.213, C:V.217, C:F.220 Hydrogen bonds: C:Y.55 Salt bridges: C:R.63, C:K.224, C:H.226, J:K.8 CDL.28: 16 residues within 4Å: Chain C: N.125, L.127, E.128, L.131, T.134, S.135, L.138, V.142 Chain G: L.23, S.27, L.30, C.31, N.34, L.37, H.38 Ligands: PEK.26 10 PLIP interactions: 5 interactions with chain G, 5 interactions with chain C Hydrophobic interactions: G:L.30, G:L.37, C:T.134, C:L.138, C:V.142 Hydrogen bonds: G:N.34, C:N.125, C:E.128 Salt bridges: G:H.38, G:H.38

3 x CHD: CHOLIC ACID(Non-covalent)

CHD.19: 8 residues within 4Å: Chain C: R.156, K.157, L.160, Q.161, F.164, F.219, L.223 Chain J: F.1 8 PLIP interactions: 6 interactions with chain C, 2 interactions with chain J Hydrophobic interactions: C:K.157, C:L.160, C:F.164, C:F.219, C:L.223, J:F.1 Salt bridges: C:R.156 Hydrogen bonds: J:F.1 CHD.20: 7 residues within 4Å: Chain A: H.233, D.300, T.301, Y.304 Chain C: W.99, H.103 Ligands: PGV.15 6 PLIP interactions: 3 interactions with chain A, 3 interactions with chain C Hydrophobic interactions: A:Y.304, C:W.99 Hydrogen bonds: A:T.301, C:W.99 Salt bridges: A:H.233, C:H.103 CHD.30: 4 residues within 4Å: Chain J: Y.32, R.33, T.37, L.40 2 PLIP interactions: 2 interactions with chain J Hydrophobic interactions: J:Y.32, J:L.40

1 x ZN: ZINC ION(Non-covalent)

ZN.24: 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

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.25: 19 residues within 4Å: Chain A: H.151, A.203 Chain C: W.34, Q.177, Y.181, Y.182, A.184, F.186, T.187, I.188, F.198, G.202, F.203 Chain G: W.62, T.68, F.69, F.70, H.71, N.76 13 PLIP interactions: 6 interactions with chain C, 6 interactions with chain G, 1 interactions with chain A Hydrophobic interactions: C:W.34, C:Q.177, C:F.203, C:F.203, A:A.203 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, G:F.69 PEK.26: 5 residues within 4Å: Chain G: S.2, A.3, K.5, H.8 Ligands: CDL.28 3 PLIP interactions: 3 interactions with chain G Hydrophobic interactions: G:A.3, G:K.5, G:K.5 PEK.27: 8 residues within 4Å: Chain C: K.157, H.158, Q.161, T.168, Y.172 Chain F: A.1 Chain G: R.17, F.21 7 PLIP interactions: 3 interactions with chain C, 4 interactions with chain G Hydrophobic interactions: C:T.168, C:Y.172, G:F.21 Hydrogen bonds: C:H.158, G:R.17 Salt bridges: G:R.17, G:R.17

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

DMU.32: 10 residues within 4Å: Chain A: L.35 Chain D: W.98, Y.102 Chain M: L.27, L.28, A.30, G.31, W.32, L.34, Y.35 9 PLIP interactions: 4 interactions with chain M, 4 interactions with chain D, 1 interactions with chain A Hydrophobic interactions: M:L.27, M:L.27, M:A.30, M:L.34, D:W.98, D:W.98, D:W.98, A:L.35 Hydrogen bonds: D:Y.102

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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