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1LYK
Asym. Unit
Info
Asym.Unit (119 KB)
Biol.Unit 1 (58 KB)
Biol.Unit 2 (59 KB)
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(1)
Title
:
THE IMPACT OF THE PHYSICAL AND CHEMICAL ENVIROMENT ON THE MOLECULAR STRUCTURE OF COPRINUS CINEREUS PEROXIDASE
Authors
:
K. Houborg, P. Harris, J. F. W. Petersen, P. Rowland, J. -C. N. Poulsen, P. Schneider, J. Vind, S. Larsen
Date
:
07 Jun 02 (Deposition) - 14 Jun 02 (Release) - 16 Nov 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.00
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. Petersen, P. Rowland, J. C. Poulsen, P. Schneider, J. Vind, S. Larsen
Impact Of The Physical And Chemical Environment On The Molecular Structure Of Coprinus Cinereus Peroxidase.
Acta Crystallogr. , Sect. D V. 59 989 2003
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Hetero Components
(6, 12)
Info
All Hetero Components
1a: BETA-D-MANNOSE (BMAa)
2a: CALCIUM ION (CAa)
2b: CALCIUM ION (CAb)
2c: CALCIUM ION (CAc)
2d: CALCIUM ION (CAd)
3a: PROTOPORPHYRIN IX CONTAINING FE (HEMa)
3b: PROTOPORPHYRIN IX CONTAINING FE (HEMb)
4a: ALPHA-D-MANNOSE (MANa)
5a: MAGNESIUM ION (MGa)
5b: MAGNESIUM ION (MGb)
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
4
Ligand/Ion
CALCIUM ION
3
HEM
2
Ligand/Ion
PROTOPORPHYRIN IX CONTAINING FE
4
MAN
1
Ligand/Ion
ALPHA-D-MANNOSE
5
MG
2
Ligand/Ion
MAGNESIUM ION
6
NAG
2
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
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Sites
(12, 12)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
GLY A:110 , ASN A:142 , HOH A:3267
BINDING SITE FOR RESIDUE NAG A 500
02
AC2
SOFTWARE
PHE A:196 , SER A:338 , LEU A:339 , ALA A:340 , HOH A:3328
BINDING SITE FOR RESIDUE BMA A 600
03
AC3
SOFTWARE
GLY B:110 , ASN B:142 , HOH B:3023
BINDING SITE FOR RESIDUE NAG B 500
04
AC4
SOFTWARE
SER B:193 , PHE B:196 , SER B:338 , LEU B:339 , ALA B:340 , HOH B:3261 , HOH B:3341
BINDING SITE FOR RESIDUE MAN B 600
05
AC5
SOFTWARE
ASP A:56 , GLY A:74 , ASP A:76 , SER A:78 , HOH A:1009 , HOH A:1027
BINDING SITE FOR RESIDUE CA A 8345
06
AC6
SOFTWARE
ASP B:56 , GLY B:74 , ASP B:76 , SER B:78 , HOH B:2009 , HOH B:2027
BINDING SITE FOR RESIDUE CA B 9345
07
AC7
SOFTWARE
SER A:184 , ASP A:201 , THR A:203 , VAL A:206 , ASP A:208
BINDING SITE FOR RESIDUE CA A 8346
08
AC8
SOFTWARE
SER B:184 , ASP B:201 , THR B:203 , VAL B:206 , ASP B:208
BINDING SITE FOR RESIDUE CA B 9346
09
AC9
SOFTWARE
ASP A:316 , HOH A:3118 , HOH B:3339
BINDING SITE FOR RESIDUE MG A 9347
10
BC1
SOFTWARE
HOH B:3127 , HOH B:3346 , HOH B:3347
BINDING SITE FOR RESIDUE MG B 9349
11
BC2
SOFTWARE
ARG A:47 , LYS A:48 , LEU A:50 , ARG A:51 , PHE A:54 , PRO A:153 , GLY A:154 , LEU A:179 , LEU A:180 , ALA A:182 , HIS A:183 , LEU A:185 , ALA A:186 , SER A:187 , GLU A:189 , GLY A:190 , LEU A:191 , MET A:242 , HOH A:1010 , HOH A:1011 , HOH A:1014 , HOH A:3009 , HOH A:3098
BINDING SITE FOR RESIDUE HEM A 344
12
BC3
SOFTWARE
ARG B:47 , LEU B:50 , ARG B:51 , PHE B:54 , PRO B:153 , GLY B:154 , ILE B:162 , LEU B:180 , ALA B:182 , HIS B:183 , LEU B:185 , ALA B:186 , SER B:187 , GLN B:188 , GLU B:189 , GLY B:190 , LEU B:191 , MET B:242 , SER B:244 , HOH B:2010 , HOH B:2011 , HOH B:2014 , HOH B:3086
BINDING SITE FOR RESIDUE HEM B 344
[
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SAPs(SNPs)/Variants
(1, 2)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_PER_COPCI_001 (I79V, chain A/B, )
View:
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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
---
---
A/B
I
79
V
* ID not provided by source
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
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PROSITE Patterns/Profiles
(3, 6)
Info
All PROSITE Patterns/Profiles
1: PEROXIDASE_2 (A:46-57,B:46-57)
2: PEROXIDASE_4 (A:49-296,B:49-296)
3: PEROXIDASE_1 (A:175-185,B:175-185)
;
View:
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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
2
A:46-57
B:46-57
2
PEROXIDASE_4
PS50873
Plant heme peroxidase family profile.
PER_COPCI
69-316
2
A:49-296
B:49-296
3
PEROXIDASE_1
PS00435
Peroxidases proximal heme-ligand signature.
PER_COPCI
195-205
2
A:175-185
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.
SCOP Domains
(1, 2)
Info
All SCOP Domains
1a: SCOP_d1lyka_ (A:)
1b: SCOP_d1lykb_ (B:)
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Protein Domains
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)
(
)
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
d1lyka_
A:
1b
d1lykb_
B:
[
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CATH Domains
(2, 4)
Info
all CATH domains
1a: CATH_1lykA01 (A:19-152,A:276-303)
1b: CATH_1lykB01 (B:19-152,B:276-303)
2a: CATH_1lykA02 (A:153-275,A:304-343)
2b: CATH_1lykB02 (B:153-275,B:304-343)
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(
)
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
1lykA01
A:19-152,A:276-303
1b
1lykB01
B:19-152,B:276-303
Topology
:
Peroxidase; domain 2
(241)
Homologous Superfamily
:
Peroxidase, domain 2
(241)
Coprinopsis cinerea. Organism_taxid: 5346.
(4)
2a
1lykA02
A:153-275,A:304-343
2b
1lykB02
B:153-275,B:304-343
[
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Pfam Domains
(2, 4)
Info
all PFAM domains
1a: PFAM_DUF3415_1lykB01 (B:266-343)
1b: PFAM_DUF3415_1lykB02 (B:266-343)
2a: PFAM_peroxidase_1lykB03 (B:28-264)
2b: PFAM_peroxidase_1lykB04 (B:28-264)
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Clans
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)
(
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(
)
Organisms
(
)
(
)
Clan
:
no clan defined [family: DUF3415]
(12)
Family
:
DUF3415
(12)
Coprinopsis cinerea (Inky cap fungus) (Hormographiella aspergillata)
(2)
1a
DUF3415-1lykB01
B:266-343
1b
DUF3415-1lykB02
B:266-343
Clan
:
no clan defined [family: peroxidase]
(92)
Family
:
peroxidase
(92)
Coprinopsis cinerea (Inky cap fungus) (Hormographiella aspergillata)
(2)
2a
peroxidase-1lykB03
B:28-264
2b
peroxidase-1lykB04
B:28-264
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Asym.Unit (119 KB)
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