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1QKS
Asym. Unit
Info
Asym.Unit (217 KB)
Biol.Unit 1 (210 KB)
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(1)
Title
:
CYTOCHROME CD1 NITRITE REDUCTASE, OXIDISED FORM
Authors
:
V. Fulop
Date
:
05 Aug 99 (Deposition) - 18 Aug 99 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.28
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Keywords
:
Enzyme, Nitrite Reductase, Oxidoreductase, Denitrification, Electron Transport, Periplasmic
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
V. Fulop, J. W. B. Moir, S. J. Ferguson, J. Hajdu
The Anatomy Of A Bifunctional Enzyme: Structural Basis For Reduction Of Oxygen To Water And Synthesys Of Nitric Oxide By Cytochrome Cd1
Cell(Cambridge, Mass. ) V. 81 369 1995
(for further references see the
PDB file header
)
[
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Hetero Components
(4, 17)
Info
All Hetero Components
1a: HEME D (DHEa)
1b: HEME D (DHEb)
2a: GLYCEROL (GOLa)
2b: GLYCEROL (GOLb)
2c: GLYCEROL (GOLc)
2d: GLYCEROL (GOLd)
2e: GLYCEROL (GOLe)
2f: GLYCEROL (GOLf)
2g: GLYCEROL (GOLg)
3a: HEME C (HECa)
3b: HEME C (HECb)
4a: SULFATE ION (SO4a)
4b: SULFATE ION (SO4b)
4c: SULFATE ION (SO4c)
4d: SULFATE ION (SO4d)
4e: SULFATE ION (SO4e)
4f: SULFATE ION (SO4f)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
DHE
2
Ligand/Ion
HEME D
2
GOL
7
Ligand/Ion
GLYCEROL
3
HEC
2
Ligand/Ion
HEME C
4
SO4
6
Ligand/Ion
SULFATE ION
[
close Hetero Component info
]
Sites
(17, 17)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ASP A:290 , GLU A:291 , GLN A:292 , HOH A:2752 , HOH A:2753 , MET B:139
BINDING SITE FOR RESIDUE SO4 A 621
02
AC2
SOFTWARE
ASN A:31 , GLN A:35 , LYS A:237 , SER A:240 , HOH A:2039 , HOH A:2754 , HOH A:2755
BINDING SITE FOR RESIDUE SO4 A 622
03
AC3
SOFTWARE
MET A:139 , ASP B:290 , GLU B:291 , GLN B:292 , HOH B:2464 , HOH B:2744
BINDING SITE FOR RESIDUE SO4 B 621
04
AC4
SOFTWARE
ASN B:31 , GLN B:35 , LYS B:237 , SER B:240 , HOH B:2745 , HOH B:2746 , HOH B:2747 , HOH B:2748
BINDING SITE FOR RESIDUE SO4 B 622
05
AC5
SOFTWARE
PHE B:395 , VAL B:396 , PRO B:449 , HOH B:2566 , HOH B:2621 , HOH B:2749 , HOH B:2750 , HOH B:2751 , HOH B:2752 , HOH B:2753
BINDING SITE FOR RESIDUE SO4 B 623
06
AC6
SOFTWARE
GLY B:439 , GLY B:440 , ASN B:461 , ILE B:466 , HOH B:2578 , HOH B:2633 , HOH B:2754 , HOH B:2755
BINDING SITE FOR RESIDUE SO4 B 624
07
AC7
SOFTWARE
ASP A:16 , HIS A:17 , ASN A:23 , ARG A:64 , CYS A:65 , CYS A:68 , HIS A:69 , GLY A:78 , LYS A:79 , LEU A:81 , LEU A:89 , TYR A:93 , LEU A:94 , PHE A:97 , SER A:102 , GOL A:611 , HOH A:2151 , HOH A:2157 , HOH A:2742 , HOH A:2743
BINDING SITE FOR RESIDUE HEC A 601
08
AC8
SOFTWARE
TYR A:25 , GLU A:26 , PRO A:27 , SER A:28 , MET A:106 , TRP A:109 , ARG A:174 , HIS A:200 , ILE A:201 , ARG A:203 , ARG A:216 , ARG A:243 , SER A:244 , TYR A:263 , ALA A:302 , HIS A:345 , ARG A:391 , PHE A:444 , GLN A:507 , THR A:554 , GLY A:555 , PHE A:557 , HOH A:2027 , HOH A:2028 , HOH A:2374 , HOH A:2377 , HOH A:2414 , HOH A:2744 , HOH A:2745 , HOH A:2746 , HOH A:2747
BINDING SITE FOR RESIDUE DHE A 602
09
AC9
SOFTWARE
ASP B:16 , HIS B:17 , ASN B:23 , ARG B:64 , CYS B:65 , CYS B:68 , HIS B:69 , GLY B:78 , LYS B:79 , LEU B:81 , LEU B:89 , TYR B:93 , LEU B:94 , PHE B:97 , SER B:102 , PRO B:103 , MET B:123 , GOL B:611 , HOH B:2152 , HOH B:2735 , HOH B:2736 , HOH B:2738
BINDING SITE FOR RESIDUE HEC B 601
10
BC1
SOFTWARE
TYR B:25 , GLU B:26 , PRO B:27 , SER B:28 , MET B:106 , TRP B:109 , ARG B:174 , HIS B:200 , ILE B:201 , ARG B:203 , ARG B:216 , ARG B:243 , SER B:244 , ILE B:245 , TYR B:263 , ALA B:302 , HIS B:345 , ARG B:391 , PHE B:444 , GLN B:507 , THR B:554 , GLY B:555 , PHE B:557 , HOH B:2382 , HOH B:2385 , HOH B:2422 , HOH B:2739 , HOH B:2740 , HOH B:2741 , HOH B:2742
BINDING SITE FOR RESIDUE DHE B 602
11
BC2
SOFTWARE
ASN A:23 , ARG A:24 , GLU A:26 , PRO A:27 , GLU A:63 , ARG A:64 , ALA A:104 , GLY A:105 , HEC A:601 , HOH A:2203
BINDING SITE FOR RESIDUE GOL A 611
12
BC3
SOFTWARE
VAL A:396 , HIS A:397 , PRO A:398 , THR A:399 , GLY A:401 , HIS A:424
BINDING SITE FOR RESIDUE GOL A 612
13
BC4
SOFTWARE
PHE A:395 , VAL A:396 , PRO A:449 , SER A:451 , ILE A:475 , HOH A:2612 , HOH A:2748 , HOH A:2749
BINDING SITE FOR RESIDUE GOL A 613
14
BC5
SOFTWARE
GLU A:136 , HOH A:2750 , HOH A:2751
BINDING SITE FOR RESIDUE GOL A 614
15
BC6
SOFTWARE
ASN B:23 , ARG B:24 , GLU B:26 , PRO B:27 , GLU B:63 , ARG B:64 , ALA B:104 , GLY B:105 , THR B:111 , HEC B:601 , HOH B:2136 , HOH B:2203
BINDING SITE FOR RESIDUE GOL B 611
16
BC7
SOFTWARE
LYS B:488 , THR B:489 , LEU B:490 , TRP B:495 , LEU B:539 , HOH B:2743
BINDING SITE FOR RESIDUE GOL B 612
17
BC8
SOFTWARE
GLU B:465 , GLY B:468 , SER B:469 , PRO B:491 , ALA B:493 , GLU B:494 , HOH B:2637
BINDING SITE FOR RESIDUE GOL B 613
[
close Site info
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
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Sorry, no Info available
[
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]
PROSITE Patterns/Profiles
(1, 2)
Info
All PROSITE Patterns/Profiles
1: CYTC (A:52-131,B:52-131)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
CYTC
PS51007
Cytochrome c family profile.
NIRS_PARPN
81-160
2
A:52-131
B:52-131
[
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]
Exons
(0, 0)
Info
All Exons
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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
(2, 4)
Info
All SCOP Domains
1a: SCOP_d1qksa1 (A:9-135)
1b: SCOP_d1qksb1 (B:9-135)
2a: SCOP_d1qksa2 (A:136-567)
2b: SCOP_d1qksb2 (B:136-567)
View:
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(
)
(
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Folds
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(
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(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
Cytochrome c
(308)
Superfamily
:
Cytochrome c
(308)
Family
:
N-terminal (heme c) domain of cytochrome cd1-nitrite reductase
(22)
Protein domain
:
N-terminal (heme c) domain of cytochrome cd1-nitrite reductase
(22)
Paracoccus denitrificans [TaxId: 266]
(2)
1a
d1qksa1
A:9-135
1b
d1qksb1
B:9-135
Class
:
All beta proteins
(24004)
Fold
:
8-bladed beta-propeller
(135)
Superfamily
:
C-terminal (heme d1) domain of cytochrome cd1-nitrite reductase
(22)
Family
:
C-terminal (heme d1) domain of cytochrome cd1-nitrite reductase
(22)
Protein domain
:
C-terminal (heme d1) domain of cytochrome cd1-nitrite reductase
(22)
Paracoccus denitrificans [TaxId: 266]
(2)
2a
d1qksa2
A:136-567
2b
d1qksb2
B:136-567
[
close SCOP info
]
CATH Domains
(2, 4)
Info
all CATH domains
1a: CATH_1qksA01 (A:36-135)
1b: CATH_1qksB01 (B:36-135)
2a: CATH_1qksA02 (A:136-567)
2b: CATH_1qksB02 (B:136-567)
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Topologies
(
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Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Mainly Alpha
(13335)
Architecture
:
Orthogonal Bundle
(10391)
Topology
:
Cytochrome Bc1 Complex; Chain D, domain 2
(279)
Homologous Superfamily
:
Cytochrome c
(279)
Paracoccus pantotrophus. Organism_taxid: 82367.
(11)
1a
1qksA01
A:36-135
1b
1qksB01
B:36-135
Class
:
Mainly Beta
(13760)
Architecture
:
8 Propellor
(110)
Topology
:
Methanol Dehydrogenase; Chain A
(110)
Homologous Superfamily
:
[code=2.140.10.20, no name defined]
(22)
Paracoccus pantotrophus. Organism_taxid: 82367.
(11)
2a
1qksA02
A:136-567
2b
1qksB02
B:136-567
[
close CATH info
]
Pfam Domains
(2, 4)
Info
all PFAM domains
1a: PFAM_Cytochrom_D1_1qksB01 (B:162-562)
1b: PFAM_Cytochrom_D1_1qksB02 (B:162-562)
2a: PFAM_Cytochrome_CBB3_1qksB03 (B:52-127)
2b: PFAM_Cytochrome_CBB3_1qksB04 (B:52-127)
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Clans
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)
(
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Families
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)
(
)
Organisms
(
)
(
)
Clan
:
Beta_propeller
(192)
Family
:
Cytochrom_D1
(5)
Paracoccus pantotrophus (Thiosphaera pantotropha)
(1)
1a
Cytochrom_D1-1qksB01
B:162-562
1b
Cytochrom_D1-1qksB02
B:162-562
Clan
:
Cytochrome-c
(108)
Family
:
Cytochrome_CBB3
(20)
Paracoccus pantotrophus (Thiosphaera pantotropha)
(1)
2a
Cytochrome_CBB3-1qksB03
B:52-127
2b
Cytochrome_CBB3-1qksB04
B:52-127
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]
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Asym.Unit (217 KB)
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