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1HJ5
Asym. Unit
Info
Asym.Unit (204 KB)
Biol.Unit 1 (198 KB)
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(1)
Title
:
CYTOCHROME CD1 NITRITE REDUCTASE, REOXIDISED ENZYME
Authors
:
T. Sjogren, J. Hajdu
Date
:
08 Jan 01 (Deposition) - 16 Jan 01 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.46
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Keywords
:
Enzyme, Nitrite Reductase, Oxidoreductase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
T. Sjogren, J. Hajdu
Structure Of The Bound Dioxygen Species In The Cytochrome Oxidase Reaction Of Cytochrome Cd1 Nitrite Reductase
J. Biol. Chem. V. 276 13072 2001
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(4, 13)
Info
All Hetero Components
1a: HEME D (DHEa)
1b: HEME D (DHEb)
2a: GLYCEROL (GOLa)
2b: GLYCEROL (GOLb)
2c: GLYCEROL (GOLc)
2d: GLYCEROL (GOLd)
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)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
DHE
2
Ligand/Ion
HEME D
2
GOL
4
Ligand/Ion
GLYCEROL
3
HEC
2
Ligand/Ion
HEME C
4
SO4
5
Ligand/Ion
SULFATE ION
[
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]
Sites
(13, 13)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ASP A:290 , GLN A:292 , 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:2439 , HOH A:2440
BINDING SITE FOR RESIDUE SO4 A 622
03
AC3
SOFTWARE
ASN B:31 , GLN B:35 , LYS B:237 , SER B:240 , HOH B:2446 , HOH B:2447 , HOH B:2448
BINDING SITE FOR RESIDUE SO4 B 622
04
AC4
SOFTWARE
TYR B:308 , ARG B:354 , LYS B:372 , HOH B:2449 , HOH B:2450
BINDING SITE FOR RESIDUE SO4 B 623
05
AC5
SOFTWARE
GLY B:439 , GLY B:440 , ASN B:461 , HOH B:2363 , HOH B:2451
BINDING SITE FOR RESIDUE SO4 B 624
06
AC6
SOFTWARE
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 , PRO A:103 , GOL A:611
BINDING SITE FOR RESIDUE HEC A 601
07
AC7
SOFTWARE
TYR A:25 , 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 , ILE A:245 , TYR A:263 , ALA A:302 , ILE A:303 , HIS A:345 , ARG A:391 , PHE A:444 , GLN A:507 , TRP A:522 , THR A:554 , GLY A:555 , PHE A:557 , HOH A:2009 , HOH A:2163 , HOH A:2164 , HOH A:2167 , HOH A:2176 , HOH A:2235 , HOH A:2434 , HOH A:2435
BINDING SITE FOR RESIDUE DHE A 602
08
AC8
SOFTWARE
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 , PHE B:97 , SER B:102 , PRO B:103 , GOL B:611 , HOH B:2054
BINDING SITE FOR RESIDUE HEC B 601
09
AC9
SOFTWARE
TYR B:25 , 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 , TYR B:263 , ALA B:302 , ILE B:303 , HIS B:345 , ARG B:391 , PHE B:444 , GLN B:507 , TRP B:522 , THR B:554 , GLY B:555 , PHE B:557 , HOH B:2008 , HOH B:2009 , HOH B:2172 , HOH B:2441 , HOH B:2442 , HOH B:2443 , HOH B:2444 , HOH B:2445
BINDING SITE FOR RESIDUE DHE B 602
10
BC1
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:2043 , HOH A:2436
BINDING SITE FOR RESIDUE GOL A 611
11
BC2
SOFTWARE
VAL A:396 , HIS A:397 , PRO A:398 , GLY A:401 , HIS A:424
BINDING SITE FOR RESIDUE GOL A 612
12
BC3
SOFTWARE
PHE A:395 , VAL A:396 , PRO A:449 , SER A:451 , ILE A:475 , HOH A:2337 , HOH A:2437
BINDING SITE FOR RESIDUE GOL A 613
13
BC4
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:2047 , HOH B:2076
BINDING SITE FOR RESIDUE GOL B 611
[
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
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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
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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_d1hj5a1 (A:9-133)
1b: SCOP_d1hj5b1 (B:9-133)
2a: SCOP_d1hj5a2 (A:134-567)
2b: SCOP_d1hj5b2 (B:134-567)
View:
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Classes
(
)
(
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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 pantotrophus [TaxId: 82367]
(11)
1a
d1hj5a1
A:9-133
1b
d1hj5b1
B:9-133
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 pantotrophus [TaxId: 82367]
(11)
2a
d1hj5a2
A:134-567
2b
d1hj5b2
B:134-567
[
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]
CATH Domains
(2, 4)
Info
all CATH domains
1a: CATH_1hj5A01 (A:36-135)
1b: CATH_1hj5B01 (B:36-135)
2a: CATH_1hj5A02 (A:136-567)
2b: CATH_1hj5B02 (B:136-567)
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Homologous Superfamilies
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)
(
)
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
1hj5A01
A:36-135
1b
1hj5B01
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
1hj5A02
A:136-567
2b
1hj5B02
B:136-567
[
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Pfam Domains
(0, 0)
Info
all PFAM domains
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Sorry, no Info available
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Asymmetric Unit 1
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