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1LYK
Biol. Unit 1
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
(3, 3)
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:
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Label:
No.
Name
Count
Type
Full Name
1
BMA
1
Ligand/Ion
BETA-D-MANNOSE
2
CA
-1
Ligand/Ion
CALCIUM ION
3
HEM
1
Ligand/Ion
PROTOPORPHYRIN IX CONTAINING FE
4
MAN
-1
Ligand/Ion
ALPHA-D-MANNOSE
5
MG
-1
Ligand/Ion
MAGNESIUM ION
6
NAG
1
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
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Sites
(6, 6)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC5 (SOFTWARE)
4: AC7 (SOFTWARE)
5: AC9 (SOFTWARE)
6: BC2 (SOFTWARE)
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No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
GLY A:110 , ASN A:142 , HOH A:3267
BINDING SITE FOR RESIDUE NAG A 500
2
AC2
SOFTWARE
PHE A:196 , SER A:338 , LEU A:339 , ALA A:340 , HOH A:3328
BINDING SITE FOR RESIDUE BMA A 600
3
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
4
AC7
SOFTWARE
SER A:184 , ASP A:201 , THR A:203 , VAL A:206 , ASP A:208
BINDING SITE FOR RESIDUE CA A 8346
5
AC9
SOFTWARE
ASP A:316 , HOH A:3118 , HOH B:3339
BINDING SITE FOR RESIDUE MG A 9347
6
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
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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 A, )
View:
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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
I
79
V
* ID not provided by source
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
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PROSITE Patterns/Profiles
(3, 3)
Info
All PROSITE Patterns/Profiles
1: PEROXIDASE_2 (A:46-57)
2: PEROXIDASE_4 (A:49-296)
3: PEROXIDASE_1 (A:175-185)
;
View:
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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
A:46-57
-
2
PEROXIDASE_4
PS50873
Plant heme peroxidase family profile.
PER_COPCI
69-316
1
A:49-296
-
3
PEROXIDASE_1
PS00435
Peroxidases proximal heme-ligand signature.
PER_COPCI
195-205
1
A:175-185
-
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Exons
(0, 0)
Info
All Exons
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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_d1lyka_ (A:)
1b: SCOP_d1lykb_ (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
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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)
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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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Chain A
Asymmetric Unit 1
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Show PDB file:
Asym.Unit (119 KB)
Header - Asym.Unit
Biol.Unit 1 (58 KB)
Header - Biol.Unit 1
Biol.Unit 2 (59 KB)
Header - Biol.Unit 2
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