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Biol. Unit 1
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Asym.Unit (227 KB)
Biol.Unit 1 (114 KB)
Biol.Unit 2 (110 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF DI-HEME PEROXIDASE FROM NITROSOMONAS EUROPAEA
Authors
:
H. Shimizu
Date
:
20 Jul 01 (Deposition) - 23 Jan 02 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.80
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,C (1x)
Biol. Unit 2: B,D (1x)
Keywords
:
Di-Heme Peroxidase, Nitrosomonas Europaea, Proteobacteria, Beta Subdivision, Ammonia-Oxidizing Bacteria, Oxidoreductase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
H. Shimizu, D. J. Schuller, W. N. Lanzilotta, M. Sundaramoorthy, D. M. Arciero, A. B. Hooper, T. L. Poulos
Crystal Structure Of Nitrosomonas Europaea Cytochrome C Peroxidase And The Structural Basis For Ligand Switching In Bacterial Di-Heme Peroxidases
Biochemistry V. 40 13483 2001
(for further references see the
PDB file header
)
[
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Hetero Components
(1, 4)
Info
All Hetero Components
1a: CALCIUM ION (CAa)
1b: CALCIUM ION (CAb)
1c: CALCIUM ION (CAc)
1d: CALCIUM ION (CAd)
1e: CALCIUM ION (CAe)
2a: GLYCEROL (GOLa)
3a: PROTOPORPHYRIN IX CONTAINING FE (HEMa)
3b: PROTOPORPHYRIN IX CONTAINING FE (HEMb)
3c: PROTOPORPHYRIN IX CONTAINING FE (HEMc)
3d: PROTOPORPHYRIN IX CONTAINING FE (HEMd)
3e: PROTOPORPHYRIN IX CONTAINING FE (HEMe)
3f: PROTOPORPHYRIN IX CONTAINING FE (HEMf)
3g: PROTOPORPHYRIN IX CONTAINING FE (HEMg)
3h: PROTOPORPHYRIN IX CONTAINING FE (HEMh)
4a: MAGNESIUM ION (MGa)
4b: MAGNESIUM ION (MGb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CA
-1
Ligand/Ion
CALCIUM ION
2
GOL
-1
Ligand/Ion
GLYCEROL
3
HEM
4
Ligand/Ion
PROTOPORPHYRIN IX CONTAINING FE
4
MG
-1
Ligand/Ion
MAGNESIUM ION
[
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Sites
(8, 8)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC5 (SOFTWARE)
5: AC8 (SOFTWARE)
6: AC9 (SOFTWARE)
7: BC3 (SOFTWARE)
8: BC4 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
ASN A:67 , THR A:239 , PRO A:241 , HOH A:1421 , HOH A:1423 , HOH A:1425 , HOH A:1426
BINDING SITE FOR RESIDUE CA A 410
2
AC2
SOFTWARE
GLN A:253 , THR A:257 , HOH A:1574
BINDING SITE FOR RESIDUE CA A 1411
3
AC3
SOFTWARE
HOH A:1454 , HOH A:1480 , HOH A:1597 , HOH A:1598 , HOH A:1654 , HOH A:1664
BINDING SITE FOR RESIDUE MG A 1420
4
AC5
SOFTWARE
ASN C:67 , THR C:239 , PRO C:241 , HOH C:411 , HOH C:415 , HOH C:417 , HOH C:433
BINDING SITE FOR RESIDUE CA C 410
5
AC8
SOFTWARE
ILE A:37 , SER A:38 , CYS A:39 , CYS A:42 , HIS A:43 , SER A:56 , ILE A:57 , ILE A:66 , PRO A:69 , ASN A:77 , GLN A:80 , PHE A:81 , TRP A:82 , ARG A:85 , LEU A:89 , GLN A:92 , PRO A:96 , GLU A:102 , ILE A:142 , GLU A:146 , LYS A:229 , HOH A:1469 , HOH A:1471 , HOH A:1499 , HOH A:1603 , HOH A:1680
BINDING SITE FOR RESIDUE HEM A 401
6
AC9
SOFTWARE
TRP A:82 , PHE A:178 , GLY A:182 , CYS A:183 , GLN A:185 , CYS A:186 , HIS A:187 , MET A:200 , PHE A:228 , PRO A:231 , LEU A:233 , ILE A:236 , TYR A:242 , PHE A:243 , HIS A:244 , MET A:258 , GLN A:262 , LEU A:263 , PHE A:267 , HOH A:1423 , HOH A:1426 , HOH A:1437 , HOH A:1458
BINDING SITE FOR RESIDUE HEM A 402
7
BC3
SOFTWARE
ILE C:37 , SER C:38 , CYS C:39 , CYS C:42 , HIS C:43 , SER C:56 , ILE C:57 , ILE C:66 , PRO C:69 , ASN C:77 , GLN C:80 , PHE C:81 , TRP C:82 , ARG C:85 , LEU C:89 , GLN C:92 , PRO C:96 , GLU C:102 , ILE C:142 , GLU C:146 , LYS C:229 , HOH C:453 , HOH C:468 , HOH C:503 , HOH C:605 , HOH C:689
BINDING SITE FOR RESIDUE HEM C 401
8
BC4
SOFTWARE
TRP C:82 , PHE C:178 , CYS C:183 , GLN C:185 , CYS C:186 , HIS C:187 , MET C:200 , PHE C:228 , PRO C:231 , LEU C:233 , ILE C:236 , PHE C:243 , HIS C:244 , MET C:258 , GLN C:262 , LEU C:263 , PHE C:267 , HOH C:413 , HOH C:415 , HOH C:433 , HOH C:436
BINDING SITE FOR RESIDUE HEM C 402
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
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Sorry, no Info available
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PROSITE Patterns/Profiles
(1, 4)
Info
All PROSITE Patterns/Profiles
1: CYTC (A:17-125,C:17-125,A:169-283,C:169-...)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
CYTC
PS51007
Cytochrome c family profile.
CCPR_NITEU
43-151
195-309
4
A:17-125
-
C:17-125
-
A:169-283
-
C:169-283
-
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Exons
(0, 0)
Info
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Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
(no "Exon" information available for biological units yet)
SCOP Domains
(1, 8)
Info
All SCOP Domains
1a: SCOP_d1iqca1 (A:1-150)
1b: SCOP_d1iqca2 (A:151-308)
1c: SCOP_d1iqcb1 (B:1-150)
1d: SCOP_d1iqcb2 (B:151-308)
1e: SCOP_d1iqcc1 (C:1-150)
1f: SCOP_d1iqcc2 (C:151-308)
1g: SCOP_d1iqcd1 (D:1-150)
1h: SCOP_d1iqcd2 (D:151-308)
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Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
Cytochrome c
(308)
Superfamily
:
Cytochrome c
(308)
Family
:
Di-heme cytochrome c peroxidase
(6)
Protein domain
:
Di-heme cytochrome c peroxidase
(6)
Nitrosomonas europaea [TaxId: 915]
(1)
1a
d1iqca1
A:1-150
1b
d1iqca2
A:151-308
1c
d1iqcb1
B:1-150
1d
d1iqcb2
B:151-308
1e
d1iqcc1
C:1-150
1f
d1iqcc2
C:151-308
1g
d1iqcd1
D:1-150
1h
d1iqcd2
D:151-308
[
close SCOP info
]
CATH Domains
(1, 8)
Info
all CATH domains
1a: CATH_1iqcA02 (A:17-164,A:303-308)
1b: CATH_1iqcB02 (B:17-164,B:303-308)
1c: CATH_1iqcC02 (C:17-164,C:303-308)
1d: CATH_1iqcD02 (D:17-164,D:303-308)
1e: CATH_1iqcA01 (A:1-16,A:165-302)
1f: CATH_1iqcB01 (B:1-16,B:165-302)
1g: CATH_1iqcC01 (C:1-16,C:165-302)
1h: CATH_1iqcD01 (D:1-16,D:165-302)
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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)
Nitrosomonas europaea. Organism_taxid: 915
(3)
1a
1iqcA02
A:17-164,A:303-308
1b
1iqcB02
B:17-164,B:303-308
1c
1iqcC02
C:17-164,C:303-308
1d
1iqcD02
D:17-164,D:303-308
1e
1iqcA01
A:1-16,A:165-302
1f
1iqcB01
B:1-16,B:165-302
1g
1iqcC01
C:1-16,C:165-302
1h
1iqcD01
D:1-16,D:165-302
[
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Pfam Domains
(0, 0)
Info
all PFAM domains
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Asymmetric Unit 1
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