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1QLE
Asym. Unit
Info
Asym.Unit (228 KB)
Biol.Unit 1 (220 KB)
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(1)
Title
:
CRYO-STRUCTURE OF THE PARACOCCUS DENITRIFICANS FOUR-SUBUNIT CYTOCHROME C OXIDASE IN THE COMPLETELY OXIDIZED STATE COMPLEXED WITH AN ANTIBODY FV FRAGMENT
Authors
:
A. Harrenga, H. Michel
Date
:
30 Aug 99 (Deposition) - 02 Dec 99 (Release) - 12 Jul 17 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
3.00
Chains
:
Asym. Unit : A,B,C,D,H,L
Biol. Unit 1: A,B,C,D,H,L (1x)
Keywords
:
Oxidoreductase/Immune System, Complex (Oxidoreductase-Antibody), Electron Transport, Transmembrane, Cytochrome Oxidase, Antibody Complex, Oxidoreductase-Immune System Complex
(Keyword Search:
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Gene Ontology, PubMed, Web (Google)
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)
Reference
:
A. Harrenga, H. Michel
The Cytochrome C Oxidase From Paracoccus Denitrificans Does Not Change The Metal Center Ligation Upon Reduction
J. Biol. Chem. V. 274 33296 1999
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Hetero Components
(6, 8)
Info
All Hetero Components
1a: CALCIUM ION (CAa)
3a: DINUCLEAR COPPER ION (CUAa)
2a: COPPER (II) ION (CUa)
4a: HEME-A (HEAa)
4b: HEME-A (HEAb)
5a: MANGANESE (II) ION (MNa)
6a: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHO... (PC1a)
6b: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHO... (PC1b)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CA
1
Ligand/Ion
CALCIUM ION
2
CU
1
Ligand/Ion
COPPER (II) ION
3
CUA
1
Ligand/Ion
DINUCLEAR COPPER ION
4
HEA
2
Ligand/Ion
HEME-A
5
MN
1
Ligand/Ion
MANGANESE (II) ION
6
PC1
2
Ligand/Ion
1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE
[
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Sites
(8, 8)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
6: AC6 (SOFTWARE)
7: AC7 (SOFTWARE)
8: AC8 (SOFTWARE)
View:
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Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
HIS A:276 , HIS A:325 , HIS A:326
BINDING SITE FOR RESIDUE CU Y 2
2
AC2
SOFTWARE
GLU A:56 , HIS A:59 , PRO A:60 , GLY A:61 , GLN A:63
BINDING SITE FOR RESIDUE CA Z 1
3
AC3
SOFTWARE
HIS A:403 , ASP A:404 , GLU B:218
BINDING SITE FOR RESIDUE MN Z 2
4
AC4
SOFTWARE
LEU A:36 , ALA A:39 , GLY A:40 , VAL A:47 , THR A:50 , ARG A:54 , TRP A:87 , ILE A:91 , HIS A:94 , MET A:98 , VAL A:103 , ALA A:106 , GLY A:163 , TRP A:164 , TYR A:406 , VAL A:409 , PHE A:412 , HIS A:413 , MET A:416 , SER A:417 , VAL A:421 , MET A:452 , ARG A:473 , ARG A:474 , TYR A:475 , PHE A:500
BINDING SITE FOR RESIDUE HEA X 1
5
AC5
SOFTWARE
TRP A:164 , VAL A:279 , TYR A:280 , HIS A:325 , HIS A:326 , ALA A:348 , THR A:351 , GLY A:387 , GLY A:390 , VAL A:391 , LEU A:393 , SER A:394 , ASP A:399 , HIS A:403 , VAL A:408 , HIS A:411 , PHE A:412 , VAL A:415 , ARG A:473 , ARG A:474 , VAL B:45 , ILE B:88
BINDING SITE FOR RESIDUE HEA X 2
6
AC6
SOFTWARE
HIS B:181 , CYS B:216 , GLU B:218 , CYS B:220 , HIS B:224 , MET B:227
BINDING SITE FOR RESIDUE CUA Y 1
7
AC7
SOFTWARE
LEU A:233 , TRP A:323 , GLN A:336 , TYR A:339 , ARG B:198 , VAL C:102 , TRP C:106 , LYS C:110 , TYR C:114 , PRO C:121 , ASP C:124 , SER D:37 , ASN D:48
BINDING SITE FOR RESIDUE PC1 P 2
8
AC8
SOFTWARE
LEU C:55 , TRP C:66 , VAL C:69 , VAL C:70 , GLY C:73 , GLU C:74 , HIS C:78 , LEU C:86 , PHE C:90 , ILE C:222 , ILE C:225 , PHE C:226 , VAL C:229 , ARG C:233 , GLN C:238 , THR C:240 , GLN C:243 , HIS C:244 , VAL C:245 , GLY C:246
BINDING SITE FOR RESIDUE PC1 P 3
[
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
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Label:
Sorry, no Info available
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PROSITE Patterns/Profiles
(6, 6)
Info
All PROSITE Patterns/Profiles
1: COX3 (C:4-273)
2: COX1 (A:22-550)
3: COX2_TM (B:12-107)
4: COX2_CUA (B:109-245)
5: COX2 (B:179-227)
6: COX1_CUB (A:272-326)
;
View:
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End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
COX3
PS50253
Heme-copper oxidase subunit III family profile.
COX3_PARDE
5-274
1
C:4-273
2
COX1
PS50855
Cytochrome oxidase subunit I profile.
COX1B_PARDE
22-550
1
A:22-550
3
COX2_TM
PS50999
Cytochrome oxidase subunit II transmembrane region profile.
COX2_PARDE
41-136
1
B:12-107
4
COX2_CUA
PS50857
Cytochrome oxidase subunit II copper A binding domain profile.
COX2_PARDE
138-274
1
B:109-245
5
COX2
PS00078
CO II and nitrous oxide reductase dinuclear copper centers signature.
COX2_PARDE
208-256
1
B:179-227
6
COX1_CUB
PS00077
Heme-copper oxidase catalytic subunit, copper B binding region signature.
COX1B_PARDE
272-326
1
A:272-326
[
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]
Exons
(0, 0)
Info
All Exons
View:
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All Exon Boundaries
View:
Label:
Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
SCOP Domains
(7, 7)
Info
All SCOP Domains
1a: SCOP_d1qleb1 (B:108-252)
2a: SCOP_d1qleh_ (H:)
3a: SCOP_d1qlel_ (L:)
4a: SCOP_d1qlea_ (A:)
5a: SCOP_d1qlec_ (C:)
6a: SCOP_d1qled_ (D:)
7a: SCOP_d1qleb2 (B:1-107)
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Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All beta proteins
(24004)
Fold
:
Cupredoxin-like
(545)
Superfamily
:
Cupredoxins
(543)
Family
:
Periplasmic domain of cytochrome c oxidase subunit II
(70)
Protein domain
:
Cytochrome c oxidase
(62)
Paracoccus denitrificans [TaxId: 266]
(4)
1a
d1qleb1
B:108-252
Fold
:
Immunoglobulin-like beta-sandwich
(7299)
Superfamily
:
Immunoglobulin
(5995)
Family
:
V set domains (antibody variable domain-like)
(1919)
Protein domain
:
Immunoglobulin heavy chain variable domain, VH
(658)
Mouse (Mus musculus), cluster 2.2 [TaxId: 10090]
(58)
2a
d1qleh_
H:
Protein domain
:
Immunoglobulin light chain kappa variable domain, VL-kappa
(616)
Mouse (Mus musculus), cluster 4 [TaxId: 10090]
(211)
3a
d1qlel_
L:
Class
:
Membrane and cell surface proteins and peptides
(2046)
Fold
:
Cytochrome c oxidase subunit I-like
(65)
Superfamily
:
Cytochrome c oxidase subunit I-like
(65)
Family
:
Cytochrome c oxidase subunit I-like
(65)
Protein domain
:
Bacterial aa3 type cytochrome c oxidase subunit I
(8)
Paracoccus denitrificans [TaxId: 266]
(2)
4a
d1qlea_
A:
Fold
:
Cytochrome c oxidase subunit III-like
(29)
Superfamily
:
Cytochrome c oxidase subunit III-like
(29)
Family
:
Cytochrome c oxidase subunit III-like
(29)
Protein domain
:
Bacterial aa3 type cytochrome c oxidase subunit III
(3)
Paracoccus denitrificans [TaxId: 266]
(1)
5a
d1qlec_
C:
Fold
:
Single transmembrane helix
(568)
Superfamily
:
Bacterial aa3 type cytochrome c oxidase subunit IV
(3)
Family
:
Bacterial aa3 type cytochrome c oxidase subunit IV
(3)
Protein domain
:
Bacterial aa3 type cytochrome c oxidase subunit IV
(3)
Paracoccus denitrificans [TaxId: 266]
(1)
6a
d1qled_
D:
Fold
:
Transmembrane helix hairpin
(84)
Superfamily
:
Cytochrome c oxidase subunit II-like, transmembrane region
(66)
Family
:
Cytochrome c oxidase subunit II-like, transmembrane region
(57)
Protein domain
:
Bacterial aa3 type cytochrome c oxidase subunit II
(10)
Paracoccus denitrificans [TaxId: 266]
(4)
7a
d1qleb2
B:1-107
[
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CATH Domains
(7, 8)
Info
all CATH domains
1a: CATH_1qleC01 (C:1-77)
2a: CATH_1qleB02 (B:25-105)
3a: CATH_1qleA00 (A:17-554)
4a: CATH_1qleC02 (C:78-273)
5a: CATH_1qleD00 (D:7-49)
6a: CATH_1qleB01 (B:1-24,B:106-252)
7a: CATH_1qleL00 (L:1-108)
7b: CATH_1qleH00 (H:1-119)
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)
Topologies
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)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Mainly Alpha
(13335)
Architecture
:
Orthogonal Bundle
(10391)
Topology
:
Helix Hairpins
(718)
Homologous Superfamily
:
[code=1.10.287.70, no name defined]
(106)
Paracoccus denitrificans. Organism_taxid: 266.
(1)
1a
1qleC01
C:1-77
Homologous Superfamily
:
[code=1.10.287.90, no name defined]
(33)
Paracoccus denitrificans. Organism_taxid: 266.
(3)
2a
1qleB02
B:25-105
Architecture
:
Up-down Bundle
(3216)
Topology
:
Cytochrome C Oxidase; Chain A
(41)
Homologous Superfamily
:
Cytochrome C Oxidase, chain A
(41)
Paracoccus denitrificans. Organism_taxid: 266.
(3)
3a
1qleA00
A:17-554
Topology
:
Four Helix Bundle (Hemerythrin (Met), subunit A)
(300)
Homologous Superfamily
:
[code=1.20.120.80, no name defined]
(26)
Paracoccus denitrificans. Organism_taxid: 266.
(1)
4a
1qleC02
C:78-273
Topology
:
Single alpha-helices involved in coiled-coils or other helix-helix interfaces
(552)
Homologous Superfamily
:
[code=1.20.5.160, no name defined]
(3)
Paracoccus denitrificans. Organism_taxid: 266.
(1)
5a
1qleD00
D:7-49
Class
:
Mainly Beta
(13760)
Architecture
:
Sandwich
(5577)
Topology
:
Immunoglobulin-like
(3897)
Homologous Superfamily
:
Cupredoxins - blue copper proteins
(420)
Paracoccus denitrificans. Organism_taxid: 266.
(20)
6a
1qleB01
B:1-24,B:106-252
Homologous Superfamily
:
Immunoglobulins
(2282)
Paracoccus denitrificans. Organism_taxid: 266.
(3)
7a
1qleL00
L:1-108
7b
1qleH00
H:1-119
[
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]
Pfam Domains
(5, 5)
Info
all PFAM domains
1a: PFAM_COX2_1qleB01 (B:112-234)
2a: PFAM_COX1_1qleA01 (A:28-496)
3a: PFAM_COX2_TM_1qleB02 (B:12-99)
4a: PFAM_COX3_1qleC01 (C:6-272)
5a: PFAM_COX4_pro_2_1qleD01 (D:9-49)
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Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
CU_oxidase
(192)
Family
:
COX2
(19)
Paracoccus denitrificans
(1)
1a
COX2-1qleB01
B:112-234
Clan
:
no clan defined [family: COX1]
(19)
Family
:
COX1
(19)
Paracoccus denitrificans
(1)
2a
COX1-1qleA01
A:28-496
Clan
:
no clan defined [family: COX2_TM]
(16)
Family
:
COX2_TM
(16)
Paracoccus denitrificans
(1)
3a
COX2_TM-1qleB02
B:12-99
Clan
:
no clan defined [family: COX3]
(12)
Family
:
COX3
(12)
Paracoccus denitrificans
(1)
4a
COX3-1qleC01
C:6-272
Clan
:
no clan defined [family: COX4_pro_2]
(3)
Family
:
COX4_pro_2
(3)
Paracoccus denitrificans
(1)
5a
COX4_pro_2-1qleD01
D:9-49
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