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1LY8
Biol. Unit 2
Info
Asym.Unit (126 KB)
Biol.Unit 1 (62 KB)
Biol.Unit 2 (62 KB)
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(1)
Title
:
THE CRYSTAL STRUCTURE OF A MUTANT ENZYME OF COPRINUS CINEREUS PEROXIDASE PROVIDES AN UNDERSTANDING OF ITS INCREASED THERMOSTABILITY AND INSIGHT INTO MODELLING OF PROTEIN STRUCTURES
Authors
:
K. Houborg, P. Harris, J. -C. N. Poulsen, A. Svendsen, P. Schneider, S. L
Date
:
07 Jun 02 (Deposition) - 14 Jun 02 (Release) - 16 Nov 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.05
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Keywords
:
Peroxidase, Mutant, Thermostability, Coprinus Cinereus, Oxidoreductase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
K. Houborg, P. Harris, J. C. Poulsen, P. Schneider, A. Svendsen, S. Larsen
The Structure Of A Mutant Enzyme Of Coprinus Cinereus Peroxidase Provides An Understanding Of Its Increased Thermostability.
Acta Crystallogr. , Sect. D V. 59 997 2003
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Hetero Components
(5, 12)
Info
All Hetero Components
1a: BETA-D-MANNOSE (BMAa)
1b: BETA-D-MANNOSE (BMAb)
2a: CALCIUM ION (CAa)
2b: CALCIUM ION (CAb)
2c: CALCIUM ION (CAc)
2d: CALCIUM ION (CAd)
3a: GLYCEROL (GOLa)
3b: GLYCEROL (GOLb)
3c: GLYCEROL (GOLc)
3d: GLYCEROL (GOLd)
3e: GLYCEROL (GOLe)
3f: GLYCEROL (GOLf)
3g: GLYCEROL (GOLg)
3h: GLYCEROL (GOLh)
3i: GLYCEROL (GOLi)
3j: GLYCEROL (GOLj)
3k: GLYCEROL (GOLk)
3l: GLYCEROL (GOLl)
4a: PROTOPORPHYRIN IX CONTAINING FE (HEMa)
4b: PROTOPORPHYRIN IX CONTAINING FE (HEMb)
5a: ALPHA-D-MANNOSE (MANa)
5b: ALPHA-D-MANNOSE (MANb)
6a: N-ACETYL-D-GLUCOSAMINE (NAGa)
6b: N-ACETYL-D-GLUCOSAMINE (NAGb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
BMA
1
Ligand/Ion
BETA-D-MANNOSE
2
CA
-1
Ligand/Ion
CALCIUM ION
3
GOL
8
Ligand/Ion
GLYCEROL
4
HEM
1
Ligand/Ion
PROTOPORPHYRIN IX CONTAINING FE
5
MAN
1
Ligand/Ion
ALPHA-D-MANNOSE
6
NAG
1
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
[
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Sites
(14, 14)
Info
All Sites
01: AC4 (SOFTWARE)
02: AC5 (SOFTWARE)
03: AC6 (SOFTWARE)
04: AC8 (SOFTWARE)
05: AC9 (SOFTWARE)
06: BC3 (SOFTWARE)
07: BC4 (SOFTWARE)
08: BC6 (SOFTWARE)
09: BC7 (SOFTWARE)
10: BC8 (SOFTWARE)
11: BC9 (SOFTWARE)
12: CC2 (SOFTWARE)
13: CC3 (SOFTWARE)
14: CC4 (SOFTWARE)
View:
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Label:
No.
Name
Evidence
Residues
Description
01
AC4
SOFTWARE
ALA B:81 , ILE B:107 , GLY B:110 , PHE B:113 , ASN B:142 , HOH B:9062 , HOH B:9118 , HOH B:9221
BINDING SITE FOR RESIDUE NAG B 500
02
AC5
SOFTWARE
THR B:313 , THR B:331
BINDING SITE FOR RESIDUE BMA B 600
03
AC6
SOFTWARE
GLY B:238 , SER B:338 , LEU B:339 , GOL B:803 , HOH B:9042 , HOH B:9074
BINDING SITE FOR RESIDUE MAN B 700
04
AC8
SOFTWARE
ASP B:56 , GLY B:74 , ASP B:76 , SER B:78 , HOH B:9017 , HOH B:9196
BINDING SITE FOR RESIDUE CA B 9002
05
AC9
SOFTWARE
SER B:184 , ASP B:201 , THR B:203 , VAL B:206 , ASP B:208
BINDING SITE FOR RESIDUE CA B 9003
06
BC3
SOFTWARE
ARG B:47 , LEU B:50 , PHE B:54 , PRO B:153 , GLY B:154 , PRO B:155 , PHE B:166 , LEU B:179 , LEU B:180 , ALA B:182 , HIS B:183 , ALA B:186 , SER B:187 , GLN B:188 , GLU B:189 , GLY B:190 , LEU B:191 , SER B:244 , MET B:276 , HOH B:9004 , HOH B:9005 , HOH B:9049 , HOH B:9131
BINDING SITE FOR RESIDUE HEM B 344
07
BC4
SOFTWARE
GLN B:38 , THR B:158 , THR B:160 , HOH B:9226 , HOH B:9265 , HOH B:9287
BINDING SITE FOR RESIDUE GOL B 800
08
BC6
SOFTWARE
HIS B:82 , ASN B:84 , ILE B:85 , HOH B:9304
BINDING SITE FOR RESIDUE GOL B 802
09
BC7
SOFTWARE
ALA B:66 , SER B:338 , MAN B:700 , HOH B:9264
BINDING SITE FOR RESIDUE GOL B 803
10
BC8
SOFTWARE
ASP B:97 , SER B:252 , ARG B:253 , HOH B:9086 , HOH B:9137 , HOH B:9151 , HOH B:9269
BINDING SITE FOR RESIDUE GOL B 804
11
BC9
SOFTWARE
HOH A:9206 , CYS B:42 , ASN B:127 , GLN B:205 , HOH B:9041 , HOH B:9175 , HOH B:9258
BINDING SITE FOR RESIDUE GOL B 805
12
CC2
SOFTWARE
SER A:264 , HOH A:9093 , SER B:260 , SER B:264 , VAL B:267 , ARG B:271
BINDING SITE FOR RESIDUE GOL B 807
13
CC3
SOFTWARE
SER B:263 , SER B:264 , ASN B:265 , GLU B:266 , PRO B:306 , HOH B:9307
BINDING SITE FOR RESIDUE GOL B 808
14
CC4
SOFTWARE
PRO B:90 , ALA B:91 , PRO B:155 , PHE B:229 , HOH B:9131
BINDING SITE FOR RESIDUE GOL B 809
[
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SAPs(SNPs)/Variants
(1, 1)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
1: VAR_PER_COPCI_001 (I79V, chain B, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_PER_COPCI_001
*
I
99
V
PER_COPCI
---
---
B
I
79
V
* ID not provided by source
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(3, 3)
Info
All PROSITE Patterns/Profiles
1: PEROXIDASE_2 (B:46-57)
2: PEROXIDASE_4 (B:50-296)
3: PEROXIDASE_1 (B:175-185)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
PEROXIDASE_2
PS00436
Peroxidases active site signature.
PER_COPCI
66-77
1
-
B:46-57
2
PEROXIDASE_4
PS50873
Plant heme peroxidase family profile.
PER_COPCI
69-316
1
-
B:50-296
3
PEROXIDASE_1
PS00435
Peroxidases proximal heme-ligand signature.
PER_COPCI
195-205
1
-
B:175-185
[
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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.
(no "Exon" information available for biological units yet)
SCOP Domains
(1, 2)
Info
All SCOP Domains
1a: SCOP_d1ly8a_ (A:)
1b: SCOP_d1ly8b_ (B:)
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(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
Heme-dependent peroxidases
(402)
Superfamily
:
Heme-dependent peroxidases
(402)
Family
:
CCP-like
(292)
Protein domain
:
Fungal peroxidase (ligninase)
(28)
Inky cap (Coprinus cinereus) [TaxId: 5346]
(5)
1a
d1ly8a_
A:
1b
d1ly8b_
B:
[
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CATH Domains
(2, 4)
Info
all CATH domains
1a: CATH_1ly8A01 (A:19-152,A:276-303)
1b: CATH_1ly8B01 (B:19-152,B:276-303)
2a: CATH_1ly8A02 (A:153-275,A:304-343)
2b: CATH_1ly8B02 (B:153-275,B:304-343)
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)
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)
Coprinopsis cinerea. Organism_taxid: 5346.
(4)
1a
1ly8A01
A:19-152,A:276-303
1b
1ly8B01
B:19-152,B:276-303
Topology
:
Peroxidase; domain 2
(241)
Homologous Superfamily
:
Peroxidase, domain 2
(241)
Coprinopsis cinerea. Organism_taxid: 5346.
(4)
2a
1ly8A02
A:153-275,A:304-343
2b
1ly8B02
B:153-275,B:304-343
[
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Pfam Domains
(0, 0)
Info
all PFAM domains
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Chain B
Asymmetric Unit 1
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