- PDB-3ag2: Bovine Heart Cytochrome c Oxidase in the Carbon Monoxide-bound Fu... -
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Basic information
Entry
Database: PDB / ID: 3ag2
Title
Bovine Heart Cytochrome c Oxidase in the Carbon Monoxide-bound Fully Reduced State at 100 K
Components
(Cytochrome c oxidase subunit ...) x 13
Keywords
OXIDOREDUCTASE / Copper / Electron transport / Formylation / Heme / Iron / Membrane / Mitochondrion / Mitochondrion inner membrane / Respiratory chain / Transmembrane / Transport / Acetylation / Transit peptide / Zinc / Isopeptide bond / Ubl conjugation
Function / homology
Function and homology information
TP53 Regulates Metabolic Genes / Cytoprotection by HMOX1 / respiratory chain complex IV assembly / mitochondrial respirasome assembly / respiratory chain complex IV / : / regulation of oxidative phosphorylation / Respiratory electron transport / cytochrome-c oxidase / : ...TP53 Regulates Metabolic Genes / Cytoprotection by HMOX1 / respiratory chain complex IV assembly / mitochondrial respirasome assembly / respiratory chain complex IV / : / regulation of oxidative phosphorylation / Respiratory electron transport / cytochrome-c oxidase / : / oxidative phosphorylation / mitochondrial electron transport, cytochrome c to oxygen / cytochrome-c oxidase activity / Mitochondrial protein degradation / electron transport coupled proton transport / ATP synthesis coupled electron transport / enzyme regulator activity / central nervous system development / mitochondrial inner membrane / oxidoreductase activity / copper ion binding / heme binding / mitochondrion / metal ion binding Similarity search - Function
Cytochrome C Oxidase; Chain F / Cytochrome c oxidase, subunit Vb / Cytochrome c oxidase, subunit VIb / Cytochrome C Oxidase; Chain D / Cytochrome c oxidase subunit IV / Cytochrome C Oxidase; Chain K / Cytochrome C Oxidase, chain K / Cytochrome c oxidase, subunit 8 / Cytochrome c oxidase, subunit VIIa / Cytochrome C Oxidase; Chain I ...Cytochrome C Oxidase; Chain F / Cytochrome c oxidase, subunit Vb / Cytochrome c oxidase, subunit VIb / Cytochrome C Oxidase; Chain D / Cytochrome c oxidase subunit IV / Cytochrome C Oxidase; Chain K / Cytochrome C Oxidase, chain K / Cytochrome c oxidase, subunit 8 / Cytochrome c oxidase, subunit VIIa / Cytochrome C Oxidase; Chain I / Mitochondrial cytochrome c oxidase subunit VIc/VIIs / Cytochrome C Oxidase; Chain G / Cytochrome c oxidase, subunit VIa / Cytochrome C Oxidase; Chain M / Cytochrome C Oxidase; Chain L / Cytochrome c oxidase subunit VIIc / Cytochrome c oxidase, subunit Va/VI / Cytochrome c oxidase, subunit III, four-helix bundle / Helix Hairpins - #90 / Cytochrome C Oxidase; Chain J / Cytochrome C Oxidase; Chain A / Cytochrome c oxidase-like, subunit I domain / Cytochrome c oxidase, subunit 8 / Cytochrome c oxidase, subunit 8 superfamily / Cytochrome oxidase c subunit VIII / Cytochrome c oxidase subunit VIIa, metazoa / Cytochrome C oxidase, subunit VIIB / Cytochrome c oxidase subunit IV / Cytochrome C oxidase, subunit VIIB domain superfamily / Mitochondrial cytochrome c oxidase subunit VIc/VIIs / Cytochrome c oxidase, subunit VIIa superfamily / Mitochondrial cytochrome c oxidase subunit VIc/VIIs superfamily / Cytochrome c oxidase subunit VIc / Cytochrome C oxidase chain VIIB / : / Cytochrome c oxidase, subunit VIa, conserved site / Cytochrome c oxidase subunit VIa signature. / Cytochrome c oxidase subunit VIIc / Cytochrome c oxidase subunit IV family / Cytochrome c oxidase subunit VIIc superfamily / Cytochrome c oxidase subunit IV superfamily / Cytochrome c oxidase subunit VIIc / Cytochrome c oxidase subunit IV / Cytochrome c oxidase, subunit VIa / Cytochrome c oxidase, subunit Va/VI / Cytochrome c oxidase, subunit VIa superfamily / Cytochrome c oxidase, subunit Va/VI superfamily / Cytochrome c oxidase subunit VIa / Cytochrome c oxidase subunit Va / Cytochrome c oxidase, subunit VIb / Cytochrome c oxidase, subunit VIb superfamily / Cytochrome oxidase c subunit VIb / Cytochrome c oxidase subunit VII / Cytochrome c oxidase subunit VII / Cytochrome c oxidase subunit 2, C-terminal / Cytochrome c oxidase subunit III domain / Cytochrome c oxidase subunit Vb, zinc binding region signature. / Cytochrome c oxidase, subunit Vb / Cytochrome c oxidase, subunit Vb superfamily / Cytochrome c oxidase subunit Vb / Cytochrome c oxidase subunit Vb, zinc binding domain profile. / Cytochrome c oxidase subunit I domain / Cytochrome c oxidase, subunit II / Cytochrome C oxidase subunit II, transmembrane domain / Cytochrome c oxidase subunit III / Cytochrome c oxidase subunit III-like / Cytochrome c oxidase, subunit III, 4-helical bundle / Cytochrome c oxidase subunit III / Heme-copper oxidase subunit III family profile. / Cytochrome c oxidase subunit III-like superfamily / Cytochrome C oxidase subunit II, transmembrane domain / Cytochrome oxidase subunit II transmembrane region profile. / Cytochrome c/quinol oxidase subunit II / Copper centre Cu(A) / CO II and nitrous oxide reductase dinuclear copper centers signature. / Cytochrome C oxidase subunit II, transmembrane domain superfamily / Cytochrome c oxidase, subunit I, copper-binding site / Heme-copper oxidase catalytic subunit, copper B binding region signature. / Cytochrome c oxidase-like, subunit I domain / Cytochrome oxidase subunit I profile. / Cytochrome c oxidase subunit I / Cytochrome c oxidase-like, subunit I superfamily / Cytochrome C and Quinol oxidase polypeptide I / Cytochrome C oxidase subunit II, periplasmic domain / Cytochrome c oxidase subunit II-like C-terminal / Cytochrome oxidase subunit II copper A binding domain profile. / Helix Hairpins - #70 / Coiled coil-helix-coiled coil-helix (CHCH) domain profile. / Cupredoxins - blue copper proteins / Four Helix Bundle (Hemerythrin (Met), subunit A) / Cupredoxin / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Few Secondary Structures / Irregular / Alpha Horseshoe / Helix Hairpins / Arc Repressor Mutant, subunit A / Up-down Bundle / Immunoglobulin-like / Sandwich Similarity search - Domain/homology
CARDIOLIPIN / CHOLIC ACID / CARBON MONOXIDE / COPPER (II) ION / DINUCLEAR COPPER ION / HEME-A / Chem-PEK / Chem-PGV / Chem-PSC / TRISTEAROYLGLYCEROL ...CARDIOLIPIN / CHOLIC ACID / CARBON MONOXIDE / COPPER (II) ION / DINUCLEAR COPPER ION / HEME-A / Chem-PEK / Chem-PGV / Chem-PSC / TRISTEAROYLGLYCEROL / Cytochrome c oxidase subunit 1 / 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 6B1 / Cytochrome c oxidase subunit 7C, mitochondrial / Cytochrome c oxidase subunit 6C / Cytochrome c oxidase subunit 7A1, mitochondrial / Cytochrome c oxidase subunit 6A2, mitochondrial / Cytochrome c oxidase subunit 8B, mitochondrial / Cytochrome c oxidase subunit 7B, mitochondrial / Cytochrome c oxidase subunit 2 Similarity search - Component
Cytochromecoxidasesubunit1 / Cytochrome c oxidase polypeptide I
Mass: 57093.852 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P00396, cytochrome-c oxidase
#2: Protein
Cytochromecoxidasesubunit2 / Cytochrome c oxidase polypeptide II
Mass: 26068.404 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P68530, cytochrome-c oxidase
#3: Protein
Cytochromecoxidasesubunit3 / Cytochrome c oxidase polypeptide III
Mass: 29957.627 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P00415, cytochrome-c oxidase
#4: Protein
Cytochromecoxidasesubunit4isoform1, mitochondrial / Cytochrome c oxidase polypeptide IV / Cytochrome c oxidase subunit IV isoform 1 / COX IV-1
Mass: 17179.646 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P00423
#5: Protein
Cytochromecoxidasesubunit5A, mitochondrial / Cytochrome c oxidase polypeptide Va
Mass: 12453.081 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P00426
#6: Protein
Cytochromecoxidasesubunit5B, mitochondrial / Cytochrome c oxidase polypeptide VIa / Cytochrome c oxidase polypeptide Vb
Mass: 10684.038 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P00428
#7: Protein
Cytochromecoxidasesubunit6A2, mitochondrial / Cytochrome c oxidase polypeptide VIa-heart / COXVIAH / Cytochrome c oxidase polypeptide VIb
Mass: 9629.782 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P07471
#8: Protein
Cytochromecoxidasesubunit6B1 / Cytochrome c oxidase polypeptide VII / Cytochrome c oxidase subunit AED / Cytochrome c oxidase ...Cytochrome c oxidase polypeptide VII / Cytochrome c oxidase subunit AED / Cytochrome c oxidase subunit VIb isoform 1 / COX VIb-1
Mass: 10039.244 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P00429
#9: Protein
Cytochromecoxidasesubunit6C / Cytochrome c oxidase polypeptide VIc / Cytochrome c oxidase subunit STA
Mass: 8537.019 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P04038
#10: Protein
Cytochromecoxidasesubunit7A1, mitochondrial / Cytochrome c oxidase subunit VIIIc / VIIIC / Cytochrome c oxidase subunit VIIa-heart / Cytochrome c ...Cytochrome c oxidase subunit VIIIc / VIIIC / Cytochrome c oxidase subunit VIIa-heart / Cytochrome c oxidase subunit VIIa-H / Cytochrome c oxidase subunit VIIa-muscle / Cytochrome c oxidase subunit VIIa-M
Mass: 6682.726 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P07470
#11: Protein
Cytochromecoxidasesubunit7B, mitochondrial / Cytochrome c oxidase polypeptide VIIb / IHQ
Mass: 6365.217 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P13183
#12: Protein/peptide
Cytochromecoxidasesubunit7C, mitochondrial / Cytochrome c oxidase polypeptide VIIIA / Cytochrome c oxidase polypeptide VIIc
Mass: 5449.396 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P00430
#13: Protein/peptide
Cytochromecoxidasesubunit8B, mitochondrial / Cytochrome c oxidase polypeptide VIII-heart / Cytochrome c oxidase subunit 8-1 / Cytochrome c ...Cytochrome c oxidase polypeptide VIII-heart / Cytochrome c oxidase subunit 8-1 / Cytochrome c oxidase subunit 8H / IX / VIIIb
Mass: 4967.756 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P10175
Resolution: 1.802→39.44 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.32 / Phase error: 25 / Stereochemistry target values: ML
Rfactor
Num. reflection
% reflection
Rfree
0.2084
30367
4.96 %
Rwork
0.1757
-
-
obs
0.1773
612646
99.54 %
Solvent computation
Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement step
Cycle: LAST / Resolution: 1.802→39.44 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
28462
0
2669
1765
32896
Refine LS restraints
Refine-ID
Type
Dev ideal
Number
X-RAY DIFFRACTION
f_bond_d
0.018
32214
X-RAY DIFFRACTION
f_angle_d
1.675
43332
X-RAY DIFFRACTION
f_dihedral_angle_d
17.83
18795
X-RAY DIFFRACTION
f_chiral_restr
0.095
4626
X-RAY DIFFRACTION
f_plane_restr
0.01
5099
LS refinement shell
Resolution (Å)
Rfactor Rwork
Num. reflection Rwork
Refine-ID
% reflection obs (%)
1.8023-1.8227
0.4212
17812
X-RAY DIFFRACTION
92
1.8227-1.8442
0.3952
19071
X-RAY DIFFRACTION
99
1.8442-1.8667
0.3719
19264
X-RAY DIFFRACTION
99
1.8667-1.8903
0.3554
19246
X-RAY DIFFRACTION
99
1.8903-1.9152
0.3284
19266
X-RAY DIFFRACTION
100
1.9152-1.9414
0.3135
19282
X-RAY DIFFRACTION
100
1.9414-1.9691
0.3035
19316
X-RAY DIFFRACTION
100
1.9691-1.9985
0.2873
19382
X-RAY DIFFRACTION
100
1.9985-2.0298
0.2657
19498
X-RAY DIFFRACTION
100
2.0298-2.063
0.2423
19319
X-RAY DIFFRACTION
100
2.063-2.0986
0.2269
19381
X-RAY DIFFRACTION
100
2.0986-2.1368
0.2104
19440
X-RAY DIFFRACTION
100
2.1368-2.1779
0.2021
19445
X-RAY DIFFRACTION
100
2.1779-2.2223
0.1931
19394
X-RAY DIFFRACTION
100
2.2223-2.2706
0.1823
19410
X-RAY DIFFRACTION
100
2.2706-2.3234
0.1717
19498
X-RAY DIFFRACTION
100
2.3234-2.3815
0.1655
19429
X-RAY DIFFRACTION
100
2.3815-2.4459
0.162
19440
X-RAY DIFFRACTION
100
2.4459-2.5179
0.1585
19483
X-RAY DIFFRACTION
100
2.5179-2.5991
0.1536
19460
X-RAY DIFFRACTION
100
2.5991-2.692
0.1484
19460
X-RAY DIFFRACTION
100
2.692-2.7998
0.1478
19485
X-RAY DIFFRACTION
100
2.7998-2.9272
0.1518
19538
X-RAY DIFFRACTION
100
2.9272-3.0814
0.153
19539
X-RAY DIFFRACTION
100
3.0814-3.2744
0.1601
19573
X-RAY DIFFRACTION
100
3.2744-3.5271
0.1555
19621
X-RAY DIFFRACTION
100
3.5271-3.8817
0.1536
19636
X-RAY DIFFRACTION
100
3.8817-4.4428
0.1398
19699
X-RAY DIFFRACTION
100
4.4428-5.5949
0.1381
19800
X-RAY DIFFRACTION
100
5.5949-39.44
0.1675
20092
X-RAY DIFFRACTION
99
Refinement TLS params.
Method: refined / Refine-ID: X-RAY DIFFRACTION
ID
L11 (°2)
L12 (°2)
L13 (°2)
L22 (°2)
L23 (°2)
L33 (°2)
S11 (Å °)
S12 (Å °)
S13 (Å °)
S21 (Å °)
S22 (Å °)
S23 (Å °)
S31 (Å °)
S32 (Å °)
S33 (Å °)
T11 (Å2)
T12 (Å2)
T13 (Å2)
T22 (Å2)
T23 (Å2)
T33 (Å2)
Origin x (Å)
Origin y (Å)
Origin z (Å)
1
0.3877
0.0177
-0.0378
0.1251
-0.0104
0.2165
-0.0079
-0.0055
0.0265
0.0074
0.0283
0.0024
0.0024
-0.0535
0.0004
0.1767
-0.0105
-0.0117
0.1334
0.0021
0.1212
61.387
310.1461
198.5301
2
0.412
0.0309
0.0596
0.2297
-0.0453
0.2215
0.0155
0.1017
-0.078
0.0395
0.0315
-0.1541
0.0088
0.0909
0.0711
0.0677
-0.041
-0.0181
0.102
-0.0746
0.1842
126.772
316.423
194.621
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Selection details
1
X-RAY DIFFRACTION
1
(chainAandresid1through514) or (chainBandresid1through227) or (chainCandresid3through261) or (chainDandresid4through147) or (chainEandresid5through109) or (chainFandresid1through98) or (chainGandresid1through84) or (chainHandresid7through85) or (chainIandresid1through73) or (chainJandresid1through58) or (chainKandresid6through54) or (chainLandresid2through47) or (chainMandresid1through43)
2
X-RAY DIFFRACTION
2
(chainNandresid1through514) or (chainOandresid1through227) or (chainPand