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3HB3
Asym. Unit
Info
Asym.Unit (207 KB)
Biol.Unit 1 (193 KB)
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(1)
Title
:
HIGH RESOLUTION CRYSTAL STRUCTURE OF PARACOCCUS DENITRIFICANS CYTOCHROME C OXIDASE
Authors
:
J. Koepke, H. Angerer, G. Peng
Date
:
04 May 09 (Deposition) - 23 Jun 09 (Release) - 23 Jun 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.25
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B,C,D (1x)
Keywords
:
Electron Transfer, Proton Transfer, Proton Pumping, Membrane Protein, Cell Inner Membrane, Cell Membrane, Copper, Disulfide Bond, Electron Transport, Heme, Hydrogen Ion Transport, Ion Transport, Iron, Membrane, Metal-Binding, Oxidoreductase, Respiratory Chain, Transmembrane, Transport, Pyrrolidone Carboxylic Acid
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
J. Koepke, E. Olkhova, H. Angerer, H. Muller, G. Peng, H. Michel
High Resolution Crystal Structure Of Paracoccus Denitrificans Cytochrome C Oxidase: New Insights Into The Active Site And The Proton Transfer Pathways
Biochim. Biophys. Acta V. 1787 635 2009
(for further references see the
PDB file header
)
[
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Hetero Components
(7, 32)
Info
All Hetero Components
1a: CALCIUM ION (CAa)
2a: COPPER (I) ION (CU1a)
2b: COPPER (I) ION (CU1b)
2c: COPPER (I) ION (CU1c)
3a: HEME-A (HEAa)
3b: HEME-A (HEAb)
4a: LAURYL DIMETHYLAMINE-N-OXIDE (LDAa)
4b: LAURYL DIMETHYLAMINE-N-OXIDE (LDAb)
4c: LAURYL DIMETHYLAMINE-N-OXIDE (LDAc)
4d: LAURYL DIMETHYLAMINE-N-OXIDE (LDAd)
4e: LAURYL DIMETHYLAMINE-N-OXIDE (LDAe)
4f: LAURYL DIMETHYLAMINE-N-OXIDE (LDAf)
4g: LAURYL DIMETHYLAMINE-N-OXIDE (LDAg)
4h: LAURYL DIMETHYLAMINE-N-OXIDE (LDAh)
4i: LAURYL DIMETHYLAMINE-N-OXIDE (LDAi)
4j: LAURYL DIMETHYLAMINE-N-OXIDE (LDAj)
5a: DODECYL-BETA-D-MALTOSIDE (LMTa)
5b: DODECYL-BETA-D-MALTOSIDE (LMTb)
5c: DODECYL-BETA-D-MALTOSIDE (LMTc)
5d: DODECYL-BETA-D-MALTOSIDE (LMTd)
5e: DODECYL-BETA-D-MALTOSIDE (LMTe)
5f: DODECYL-BETA-D-MALTOSIDE (LMTf)
5g: DODECYL-BETA-D-MALTOSIDE (LMTg)
5h: DODECYL-BETA-D-MALTOSIDE (LMTh)
5i: DODECYL-BETA-D-MALTOSIDE (LMTi)
5j: DODECYL-BETA-D-MALTOSIDE (LMTj)
5k: DODECYL-BETA-D-MALTOSIDE (LMTk)
5l: DODECYL-BETA-D-MALTOSIDE (LMTl)
5m: DODECYL-BETA-D-MALTOSIDE (LMTm)
5n: DODECYL-BETA-D-MALTOSIDE (LMTn)
6a: MANGANESE (II) ION (MNa)
7a: HYDROGEN PEROXIDE (PEOa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CA
1
Ligand/Ion
CALCIUM ION
2
CU1
3
Ligand/Ion
COPPER (I) ION
3
HEA
2
Ligand/Ion
HEME-A
4
LDA
10
Ligand/Ion
LAURYL DIMETHYLAMINE-N-OXIDE
5
LMT
14
Ligand/Ion
DODECYL-BETA-D-MALTOSIDE
6
MN
1
Ligand/Ion
MANGANESE (II) ION
7
PEO
1
Ligand/Ion
HYDROGEN PEROXIDE
[
close Hetero Component info
]
Sites
(31, 31)
Info
All Sites
01: AC1 (SOFTWARE)
02: AC2 (SOFTWARE)
03: AC3 (SOFTWARE)
04: AC4 (SOFTWARE)
05: AC5 (SOFTWARE)
06: AC6 (SOFTWARE)
07: AC7 (SOFTWARE)
08: AC8 (SOFTWARE)
09: AC9 (SOFTWARE)
10: BC1 (SOFTWARE)
11: BC2 (SOFTWARE)
12: BC3 (SOFTWARE)
13: BC4 (SOFTWARE)
14: BC5 (SOFTWARE)
15: BC6 (SOFTWARE)
16: BC7 (SOFTWARE)
17: BC8 (SOFTWARE)
18: BC9 (SOFTWARE)
19: CC1 (SOFTWARE)
20: CC2 (SOFTWARE)
21: CC3 (SOFTWARE)
22: CC4 (SOFTWARE)
23: CC5 (SOFTWARE)
24: CC6 (SOFTWARE)
25: CC7 (SOFTWARE)
26: CC8 (SOFTWARE)
27: CC9 (SOFTWARE)
28: DC1 (SOFTWARE)
29: DC2 (SOFTWARE)
30: DC3 (SOFTWARE)
31: DC4 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
LEU A:36 , THR A:50 , MET A:53 , ARG A:54 , TRP A:87 , ILE A:91 , HIS A:94 , MET A:98 , MET A:99 , VAL A:103 , GLY A:163 , TRP A:164 , TYR A:406 , PHE A:412 , HIS A:413 , MET A:416 , SER A:417 , ILE A:424 , MET A:452 , ILE A:459 , PHE A:460 , GLN A:463 , ARG A:473 , ARG A:474 , TYR A:475 , SER A:496 , HOH A:584 , HOH A:623
BINDING SITE FOR RESIDUE HEA A 559
02
AC2
SOFTWARE
TRP A:164 , TRP A:272 , VAL A:279 , TYR A:280 , HIS A:325 , HIS A:326 , THR A:351 , GLY A:352 , GLY A:387 , GLY A:390 , LEU A:393 , SER A:394 , ASP A:399 , HIS A:403 , VAL A:408 , HIS A:411 , PHE A:412 , VAL A:415 , MET A:416 , ARG A:473 , PEO A:576 , HOH A:582 , HOH A:583 , HOH A:950 , HOH A:959 , VAL B:45 , ILE B:88
BINDING SITE FOR RESIDUE HEA A 560
03
AC3
SOFTWARE
HIS A:276 , HIS A:325 , HIS A:326 , PEO A:576
BINDING SITE FOR RESIDUE CU1 A 561
04
AC4
SOFTWARE
HIS A:403 , ASP A:404 , HOH A:578 , GLU B:218 , HOH B:285 , HOH B:884
BINDING SITE FOR RESIDUE MN A 562
05
AC5
SOFTWARE
GLU A:56 , HIS A:59 , GLY A:61 , GLN A:63 , HOH A:851 , HOH A:965
BINDING SITE FOR RESIDUE CA A 563
06
AC6
SOFTWARE
ASN A:457 , PHE A:461 , LMT A:572 , LMT B:279
BINDING SITE FOR RESIDUE LDA A 564
07
AC7
SOFTWARE
LEU A:72 , ILE A:73 , LDA A:567 , LMT A:571
BINDING SITE FOR RESIDUE LDA A 565
08
AC8
SOFTWARE
GLN A:336
BINDING SITE FOR RESIDUE LDA A 566
09
AC9
SOFTWARE
TYR A:52 , ALA A:70 , LEU A:72 , LDA A:565
BINDING SITE FOR RESIDUE LDA A 567
10
BC1
SOFTWARE
TRP A:443 , LEU A:447 , PHE A:502 , LMT A:569 , HOH A:779
BINDING SITE FOR RESIDUE LMT A 568
11
BC2
SOFTWARE
PRO A:441 , TRP A:443 , GLY A:505 , TYR A:509 , LMT A:568 , VAL D:9
BINDING SITE FOR RESIDUE LMT A 569
12
BC3
SOFTWARE
ARG A:21 , LYS A:29 , LEU A:36 , MET A:435 , LEU A:511 , PRO A:537 , LMT A:575 , HOH A:964
BINDING SITE FOR RESIDUE LMT A 570
13
BC4
SOFTWARE
GLN A:58 , HIS A:59 , GLN A:63 , TYR A:64 , ALA A:74 , TYR A:494 , PHE A:497 , LDA A:565 , LMT A:572 , HOH A:593 , HOH A:771 , HOH A:787
BINDING SITE FOR RESIDUE LMT A 571
14
BC5
SOFTWARE
TYR A:484 , ASN A:487 , ILE A:488 , ILE A:491 , LDA A:564 , LMT A:571 , HOH A:787 , HOH A:1306 , HOH A:1325
BINDING SITE FOR RESIDUE LMT A 572
15
BC6
SOFTWARE
ILE A:367 , GLU A:368 , PHE A:369 , PHE A:377 , ASN B:61 , ARG B:62 , ARG B:63
BINDING SITE FOR RESIDUE LMT A 573
16
BC7
SOFTWARE
MET A:24 , LEU A:130 , LEU A:133
BINDING SITE FOR RESIDUE LMT A 574
17
BC8
SOFTWARE
TRP A:22 , ARG A:438 , LEU A:511 , PHE A:512 , ARG A:516 , LMT A:570
BINDING SITE FOR RESIDUE LMT A 575
18
BC9
SOFTWARE
HIS A:276 , HIS A:325 , HIS A:326 , HEA A:560 , CU1 A:561
BINDING SITE FOR RESIDUE PEO A 576
19
CC1
SOFTWARE
CYS B:216 , GLU B:218 , CYS B:220 , HIS B:224 , CU1 B:271
BINDING SITE FOR RESIDUE CU1 B 270
20
CC2
SOFTWARE
HIS B:181 , CYS B:216 , CYS B:220 , MET B:227 , CU1 B:270
BINDING SITE FOR RESIDUE CU1 B 271
21
CC3
SOFTWARE
THR A:389 , HIS A:464 , ASN B:19 , LDA B:274
BINDING SITE FOR RESIDUE LDA B 272
22
CC4
SOFTWARE
HIS B:36 , PHE B:37 , LDA B:276
BINDING SITE FOR RESIDUE LDA B 273
23
CC5
SOFTWARE
TYR B:40 , LDA B:272 , HOH B:1291
BINDING SITE FOR RESIDUE LDA B 274
24
CC6
SOFTWARE
ARG B:102 , LMT B:278 , LMT B:280
BINDING SITE FOR RESIDUE LDA B 275
25
CC7
SOFTWARE
HIS B:36 , TYR B:40 , LDA B:273
BINDING SITE FOR RESIDUE LDA B 276
26
CC8
SOFTWARE
PRO B:98 , ARG B:102 , GLU B:105 , LDA B:275
BINDING SITE FOR RESIDUE LMT B 278
27
CC9
SOFTWARE
PHE A:461 , TYR A:484 , TRP A:485 , LDA A:564 , ASN B:15 , GLY B:16 , MET B:18
BINDING SITE FOR RESIDUE LMT B 279
28
DC1
SOFTWARE
TRP B:33 , LEU B:87 , ILE B:99 , LDA B:275 , HOH B:1058 , HOH B:1118 , ASN D:28
BINDING SITE FOR RESIDUE LMT B 280
29
DC2
SOFTWARE
TRP A:363 , LEU B:52 , HIS B:73 , ASN B:74 , TRP B:81 , GLU B:140 , GLU B:142 , LMT B:283
BINDING SITE FOR RESIDUE LMT B 281
30
DC3
SOFTWARE
LEU A:342 , THR A:346 , VAL A:349 , VAL B:86 , LEU B:89
BINDING SITE FOR RESIDUE LMT B 282
31
DC4
SOFTWARE
PHE A:356 , PHE B:48 , LEU B:51 , LEU B:52 , ILE B:55 , ILE B:80 , VAL B:84 , LMT B:281 , HOH B:1330
BINDING SITE FOR RESIDUE LMT B 283
[
close Site info
]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(5, 5)
Info
All PROSITE Patterns/Profiles
1: COX1 (A:22-545)
2: COX2_TM (B:12-107)
3: COX2_CUA (B:109-245)
4: COX2 (B:179-227)
5: COX1_CUB (A:272-326)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
COX1
PS50855
Cytochrome oxidase subunit I profile.
COX1B_PARDE
22-550
1
A:22-545
2
COX2_TM
PS50999
Cytochrome oxidase subunit II transmembrane region profile.
COX2_PARDE
41-136
1
B:12-107
3
COX2_CUA
PS50857
Cytochrome oxidase subunit II copper A binding domain profile.
COX2_PARDE
138-274
1
B:109-245
4
COX2
PS00078
CO II and nitrous oxide reductase dinuclear copper centers signature.
COX2_PARDE
208-256
1
B:179-227
5
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
(4, 5)
Info
All SCOP Domains
1a: SCOP_d3hb3b2 (B:108-252)
2a: SCOP_d3hb3c_ (C:)
2b: SCOP_d3hb3d_ (D:)
3a: SCOP_d3hb3a_ (A:)
4a: SCOP_d3hb3b1 (B:1-107)
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Classes
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)
(
)
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
d3hb3b2
B:108-252
Fold
:
Immunoglobulin-like beta-sandwich
(7299)
Superfamily
:
Immunoglobulin
(5995)
Family
:
V set domains (antibody variable domain-like)
(1919)
Protein domain
:
automated matches
(311)
Mouse (Mus musculus) [TaxId: 10090]
(112)
2a
d3hb3c_
C:
2b
d3hb3d_
D:
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
:
automated matches
(24)
Paracoccus denitrificans [TaxId: 266]
(2)
3a
d3hb3a_
A:
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)
4a
d3hb3b1
B:1-107
[
close SCOP info
]
CATH Domains
(4, 4)
Info
all CATH domains
1a: CATH_3hb3B02 (B:25-105)
2a: CATH_3hb3A00 (A:17-545)
3a: CATH_3hb3B01 (B:1-24,B:106-252)
4a: CATH_3hb3C00 (C:1-118)
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Topologies
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Homologous Superfamilies
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)
(
)
Organisms
(
)
(
)
Class
:
Mainly Alpha
(13335)
Architecture
:
Orthogonal Bundle
(10391)
Topology
:
Helix Hairpins
(718)
Homologous Superfamily
:
[code=1.10.287.90, no name defined]
(33)
Paracoccus denitrificans. Organism_taxid: 266.
(3)
1a
3hb3B02
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)
2a
3hb3A00
A:17-545
Class
:
Mainly Beta
(13760)
Architecture
:
Sandwich
(5577)
Topology
:
Immunoglobulin-like
(3897)
Homologous Superfamily
:
Cupredoxins - blue copper proteins
(420)
Paracoccus denitrificans. Organism_taxid: 266.
(20)
3a
3hb3B01
B:1-24,B:106-252
Homologous Superfamily
:
Immunoglobulins
(2282)
Paracoccus denitrificans. Organism_taxid: 266.
(3)
4a
3hb3C00
C:1-118
[
close CATH info
]
Pfam Domains
(0, 0)
Info
all PFAM domains
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