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1ITK
Biol. Unit 2
Info
Asym.Unit (260 KB)
Biol.Unit 1 (253 KB)
Biol.Unit 2 (503 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF CATALASE-PEROXIDASE FROM HALOARCULA MARISMORTUI
Authors
:
Y. Yamada, T. Fujiwara, T. Sato, N. Igarashi, N. Tanaka
Date
:
18 Jan 02 (Deposition) - 28 Aug 02 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.00
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Biol. Unit 2: A,B (2x)
Keywords
:
Heme Protein, Oxidoreductase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
Y. Yamada, T. Fujiwara, T. Sato, N. Igarashi, N. Tanaka
The 2. 0 A Crystal Structure Of Catalase-Peroxidase From Haloarcula Marismortui.
Nat. Struct. Biol. V. 9 691 2002
(for further references see the
PDB file header
)
[
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Hetero Components
(3, 28)
Info
All Hetero Components
1a: CHLORIDE ION (CLa)
1b: CHLORIDE ION (CLb)
1c: CHLORIDE ION (CLc)
1d: CHLORIDE ION (CLd)
1e: CHLORIDE ION (CLe)
1f: CHLORIDE ION (CLf)
1g: CHLORIDE ION (CLg)
1h: CHLORIDE ION (CLh)
1i: CHLORIDE ION (CLi)
1j: CHLORIDE ION (CLj)
1k: CHLORIDE ION (CLk)
1l: CHLORIDE ION (CLl)
1m: CHLORIDE ION (CLm)
1n: CHLORIDE ION (CLn)
1o: CHLORIDE ION (CLo)
1p: CHLORIDE ION (CLp)
2a: PROTOPORPHYRIN IX CONTAINING FE (HEMa)
2b: PROTOPORPHYRIN IX CONTAINING FE (HEMb)
3a: SULFATE ION (SO4a)
3b: SULFATE ION (SO4b)
3c: SULFATE ION (SO4c)
3d: SULFATE ION (SO4d)
3e: SULFATE ION (SO4e)
3f: SULFATE ION (SO4f)
4a: UNKNOWN ATOM OR ION (UNXa)
4b: UNKNOWN ATOM OR ION (UNXb)
4c: UNKNOWN ATOM OR ION (UNXc)
4d: UNKNOWN ATOM OR ION (UNXd)
4e: UNKNOWN ATOM OR ION (UNXe)
4f: UNKNOWN ATOM OR ION (UNXf)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CL
-1
Ligand/Ion
CHLORIDE ION
2
HEM
4
Ligand/Ion
PROTOPORPHYRIN IX CONTAINING FE
3
SO4
12
Ligand/Ion
SULFATE ION
4
UNX
12
Ligand/Ion
UNKNOWN ATOM OR ION
[
close Hetero Component info
]
Sites
(30, 30)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
GLN A:239 , ARG A:243 , HOH A:2349
BINDING SITE FOR RESIDUE SO4 A 732
02
AC2
SOFTWARE
PRO A:282 , ILE A:283 , ARG B:684
BINDING SITE FOR RESIDUE SO4 A 733
03
AC3
SOFTWARE
LYS A:580 , ILE A:592 , THR A:593 , ARG A:594
BINDING SITE FOR RESIDUE SO4 A 734
04
AC4
SOFTWARE
ARG A:684 , HOH A:2724 , PRO B:282 , ILE B:283 , HOH B:2473
BINDING SITE FOR RESIDUE SO4 A 735
05
AC5
SOFTWARE
GLN B:239 , ARG B:243 , HOH B:2372
BINDING SITE FOR RESIDUE SO4 B 732
06
AC6
SOFTWARE
LYS B:580 , ILE B:592 , THR B:593 , ARG B:594 , HOH B:2192
BINDING SITE FOR RESIDUE SO4 B 733
07
AC7
SOFTWARE
SER A:212 , ASN A:220 , PRO A:224 , ASN A:236
BINDING SITE FOR RESIDUE CL A 2001
08
AC8
SOFTWARE
SER A:612 , GLY B:44
BINDING SITE FOR RESIDUE CL A 2002
09
AC9
SOFTWARE
GLY A:44 , SER B:612
BINDING SITE FOR RESIDUE CL B 2003
10
BC1
SOFTWARE
VAL A:581 , ASP A:582 , GLY A:583 , ASN A:603 , HOH A:2155
BINDING SITE FOR RESIDUE CL A 2004
11
BC2
SOFTWARE
TRP A:331 , LYS A:376 , ARG A:377
BINDING SITE FOR RESIDUE CL A 2005
12
BC3
SOFTWARE
PRO A:566 , GLU A:567 , THR A:569 , ALA A:571 , PRO A:572 , HOH A:2086 , HOH A:2319
BINDING SITE FOR RESIDUE CL A 2006
13
BC4
SOFTWARE
TRP A:187 , LYS B:21
BINDING SITE FOR RESIDUE CL A 2007
14
BC5
SOFTWARE
LYS A:710 , GLU B:47 , GLN B:145
BINDING SITE FOR RESIDUE CL B 2008
15
BC6
SOFTWARE
GLU A:47 , GLN A:145 , HOH A:2591 , LYS B:710
BINDING SITE FOR RESIDUE CL A 2009
16
BC7
SOFTWARE
LYS A:21 , TRP B:187
BINDING SITE FOR RESIDUE CL A 2010
17
BC8
SOFTWARE
GLU A:491 , HOH A:2129
BINDING SITE FOR RESIDUE CL A 2011
18
BC9
SOFTWARE
GLY A:481 , ARG A:487 , PHE A:574 , HOH A:2057 , HOH A:2062 , HOH A:2169
BINDING SITE FOR RESIDUE CL A 2012
19
CC1
SOFTWARE
HOH A:2215
BINDING SITE FOR RESIDUE CL A 2013
20
CC2
SOFTWARE
ASN A:220 , HOH A:2044
BINDING SITE FOR RESIDUE CL A 2014
21
CC3
SOFTWARE
GLY B:108
BINDING SITE FOR RESIDUE CL B 2015
22
CC4
SOFTWARE
VAL B:581 , ASP B:582 , GLY B:583 , ASN B:603 , HOH B:2256
BINDING SITE FOR RESIDUE CL B 2016
23
CC5
SOFTWARE
TRP A:429 , HOH A:2095 , HOH A:2632
BINDING SITE FOR RESIDUE UNX A 2017
24
CC6
SOFTWARE
SER B:212 , ASN B:220 , PRO B:224 , ASN B:236
BINDING SITE FOR RESIDUE UNX B 2018
25
CC7
SOFTWARE
GLY B:481 , ARG B:487 , PHE B:574 , HOH B:2046 , HOH B:2160 , HOH B:2165
BINDING SITE FOR RESIDUE UNX B 2019
26
CC8
SOFTWARE
TRP B:331 , LYS B:376 , ARG B:377
BINDING SITE FOR RESIDUE UNX B 2020
27
CC9
SOFTWARE
VAL B:213 , ASN B:220 , HOH B:2148 , HOH B:2301
BINDING SITE FOR RESIDUE UNX B 2021
28
DC1
SOFTWARE
MET B:427 , TRP B:429 , HOH B:2227
BINDING SITE FOR RESIDUE UNX B 2022
29
DC2
SOFTWARE
PRO A:88 , LEU A:89 , ARG A:92 , TRP A:95 , PRO A:221 , LEU A:254 , ILE A:255 , GLY A:258 , HIS A:259 , PHE A:261 , GLY A:262 , LYS A:263 , VAL A:264 , HIS A:265 , THR A:304 , SER A:305 , TRP A:311 , THR A:371 , TRP A:403 , HOH A:2019 , HOH A:2071 , HOH A:2102 , HOH A:2645
BINDING SITE FOR RESIDUE HEM A 800
30
DC3
SOFTWARE
PRO B:88 , TRP B:95 , PRO B:221 , LEU B:254 , ILE B:255 , GLY B:258 , HIS B:259 , GLY B:262 , LYS B:263 , VAL B:264 , HIS B:265 , THR B:304 , SER B:305 , TRP B:311 , THR B:371 , PHE B:399 , TRP B:403 , HOH B:2042 , HOH B:2117 , HOH B:2210
BINDING SITE FOR RESIDUE HEM B 800
[
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]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
[
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PROSITE Patterns/Profiles
(2, 8)
Info
All PROSITE Patterns/Profiles
1: PEROXIDASE_2 (A:87-98,B:87-98)
2: PEROXIDASE_1 (A:251-261,B:251-261)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
PEROXIDASE_2
PS00436
Peroxidases active site signature.
KATG2_HALMA
87-98
4
A:87-98
B:87-98
2
PEROXIDASE_1
PS00435
Peroxidases proximal heme-ligand signature.
KATG2_HALMA
251-261
4
A:251-261
B:251-261
[
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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.
(no "Exon" information available for biological units yet)
SCOP Domains
(1, 4)
Info
All SCOP Domains
1a: SCOP_d1itka1 (A:18-423)
1b: SCOP_d1itka2 (A:424-731)
1c: SCOP_d1itkb1 (B:18-423)
1d: SCOP_d1itkb2 (B:424-731)
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Classes
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)
(
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(
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(
)
Families
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)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
Heme-dependent peroxidases
(402)
Superfamily
:
Heme-dependent peroxidases
(402)
Family
:
Catalase-peroxidase KatG
(26)
Protein domain
:
Catalase-peroxidase KatG
(23)
Haloarcula marismortui [TaxId: 2238]
(1)
1a
d1itka1
A:18-423
1b
d1itka2
A:424-731
1c
d1itkb1
B:18-423
1d
d1itkb2
B:424-731
[
close SCOP info
]
CATH Domains
(2, 8)
Info
all CATH domains
1a: CATH_1itkA03 (A:436-580,A:710-731)
1b: CATH_1itkB03 (B:436-580,B:710-731)
1c: CATH_1itkA01 (A:53-182,A:403-414)
1d: CATH_1itkB01 (B:53-182,B:403-414)
2a: CATH_1itkA04 (A:581-709)
2b: CATH_1itkB04 (B:581-709)
2c: CATH_1itkA02 (A:233-266,A:303-402)
2d: CATH_1itkB02 (B:233-266,B:303-402)
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Classes
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Architectures
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Topologies
(
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(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Mainly Alpha
(13335)
Architecture
:
Orthogonal Bundle
(10391)
Topology
:
Peroxidase; domain 1
(244)
Homologous Superfamily
:
[code=1.10.520.10, no name defined]
(241)
Haloarcula marismortui. Organism_taxid: 2238
(1)
1a
1itkA03
A:436-580,A:710-731
1b
1itkB03
B:436-580,B:710-731
1c
1itkA01
A:53-182,A:403-414
1d
1itkB01
B:53-182,B:403-414
Topology
:
Peroxidase; domain 2
(241)
Homologous Superfamily
:
Peroxidase, domain 2
(241)
Haloarcula marismortui. Organism_taxid: 2238
(1)
2a
1itkA04
A:581-709
2b
1itkB04
B:581-709
2c
1itkA02
A:233-266,A:303-402
2d
1itkB02
B:233-266,B:303-402
[
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]
Pfam Domains
(0, 0)
Info
all PFAM domains
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Sorry, no Info available
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