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1YYG
Asym. Unit
Info
Asym.Unit (74 KB)
Biol.Unit 1 (69 KB)
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(1)
Title
:
MANGANESE PEROXIDASE COMPLEXED WITH CD(II) INHIBITOR
Authors
:
M. Sundaramoorthy, H. L. Youngs, M. H. Gold, T. L. Poulos
Date
:
24 Feb 05 (Deposition) - 10 May 05 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.60
Chains
:
Asym. Unit : A
Biol. Unit 1: A (1x)
Keywords
:
Peroxidase, Heme Enzyme, Mn(Ii) Binding Protein, Glycosylation, Oxidoreductase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
M. Sundaramoorthy, H. L. Youngs, M. H. Gold, T. L. Poulos
High-Resolution Crystal Structure Of Manganese Peroxidase: Substrate And Inhibitor Complexes.
Biochemistry V. 44 6463 2005
(for further references see the
PDB file header
)
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Hetero Components
(6, 11)
Info
All Hetero Components
1a: CALCIUM ION (CAa)
1b: CALCIUM ION (CAb)
1c: CALCIUM ION (CAc)
2a: GLYCEROL (GOLa)
2b: GLYCEROL (GOLb)
2c: GLYCEROL (GOLc)
3a: PROTOPORPHYRIN IX CONTAINING FE (HEMa)
4a: ALPHA-D-MANNOSE (MANa)
6a: N-ACETYL-D-GLUCOSAMINE (NAGa)
6b: N-ACETYL-D-GLUCOSAMINE (NAGb)
5a: SODIUM ION (NAa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CA
3
Ligand/Ion
CALCIUM ION
2
GOL
3
Ligand/Ion
GLYCEROL
3
HEM
1
Ligand/Ion
PROTOPORPHYRIN IX CONTAINING FE
4
MAN
1
Ligand/Ion
ALPHA-D-MANNOSE
5
NA
1
Ligand/Ion
SODIUM ION
6
NAG
2
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
[
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Sites
(11, 11)
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)
View:
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Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
LEU A:69 , ASN A:98 , THR A:99 , ILE A:100 , ASN A:131 , NAG A:362 , GOL A:404 , HOH A:1090 , HOH A:1118 , HOH A:1248 , HOH A:1313
BINDING SITE FOR RESIDUE NAG A 361
02
AC2
SOFTWARE
MET A:94 , GLN A:95 , ASN A:98 , NAG A:361 , GOL A:404 , HOH A:1233 , HOH A:1406 , HOH A:1533
BINDING SITE FOR RESIDUE NAG A 362
03
AC3
SOFTWARE
HIS A:11 , PRO A:331 , GLY A:332 , SER A:334 , GLN A:335 , SER A:336 , HOH A:1442 , HOH A:1564
BINDING SITE FOR RESIDUE MAN A 364
04
AC4
SOFTWARE
SER A:174 , ASP A:191 , THR A:193 , THR A:196 , ASP A:198
BINDING SITE FOR RESIDUE CA A 371
05
AC5
SOFTWARE
ASP A:47 , GLY A:62 , ASP A:64 , SER A:66 , HOH A:1085 , HOH A:1128
BINDING SITE FOR RESIDUE CA A 372
06
AC6
SOFTWARE
GLU A:35 , GLU A:39 , ASP A:179 , HEM A:396 , HOH A:1040 , HOH A:1109
BINDING SITE FOR RESIDUE CA A 381
07
AC7
SOFTWARE
ASP A:84 , ALA A:357 , HOH A:1507
BINDING SITE FOR RESIDUE NA A 382
08
AC8
SOFTWARE
GLU A:35 , HIS A:38 , GLU A:39 , ARG A:42 , PHE A:45 , GLU A:143 , PRO A:144 , LEU A:169 , LEU A:170 , SER A:172 , HIS A:173 , VAL A:175 , ALA A:176 , ARG A:177 , ALA A:178 , ASP A:179 , LYS A:180 , VAL A:181 , PHE A:190 , CA A:381 , HOH A:1074 , HOH A:1109 , HOH A:1138 , HOH A:1195 , HOH A:1229
BINDING SITE FOR RESIDUE HEM A 396
09
AC9
SOFTWARE
ASP A:23 , THR A:27 , PRO A:92 , LYS A:96 , GLU A:156 , HOH A:1092 , HOH A:1299
BINDING SITE FOR RESIDUE GOL A 401
10
BC1
SOFTWARE
NAG A:361 , NAG A:362 , HOH A:1473 , HOH A:1589
BINDING SITE FOR RESIDUE GOL A 404
11
BC2
SOFTWARE
PHE A:164 , HOH A:1115 , HOH A:1129
BINDING SITE FOR RESIDUE GOL A 406
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
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Sorry, no Info available
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PROSITE Patterns/Profiles
(3, 3)
Info
All PROSITE Patterns/Profiles
1: PEROXIDASE_2 (A:37-48)
2: PEROXIDASE_4 (A:37-293)
3: PEROXIDASE_1 (A:165-175)
;
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.
PEM1_PHACH
58-69
1
A:37-48
2
PEROXIDASE_4
PS50873
Plant heme peroxidase family profile.
PEM1_PHACH
58-314
1
A:37-293
3
PEROXIDASE_1
PS00435
Peroxidases proximal heme-ligand signature.
PEM1_PHACH
186-196
1
A:165-175
[
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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, 1)
Info
All SCOP Domains
1a: SCOP_d1yyga_ (A:)
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Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
Heme-dependent peroxidases
(402)
Superfamily
:
Heme-dependent peroxidases
(402)
Family
:
CCP-like
(292)
Protein domain
:
automated matches
(48)
Basidomycetes fungus (Phanerochaete chrysosporium) [TaxId: 5306]
(6)
1a
d1yyga_
A:
[
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]
CATH Domains
(2, 2)
Info
all CATH domains
1a: CATH_1yygA01 (A:11-141,A:273-300)
2a: CATH_1yygA02 (A:142-272,A:302-342)
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(
)
Homologous Superfamilies
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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)
Phanerochaete chrysosporium. Organism_taxid: 5306
(5)
1a
1yygA01
A:11-141,A:273-300
Topology
:
Peroxidase; domain 2
(241)
Homologous Superfamily
:
Peroxidase, domain 2
(241)
Phanerochaete chrysosporium. Organism_taxid: 5306
(5)
2a
1yygA02
A:142-272,A:302-342
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Pfam Domains
(0, 0)
Info
all PFAM domains
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Sorry, no Info available
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Protein
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Protein & NOT Variant
Protein & NOT Site
Protein & NOT PROSITE
Chain A
Asymmetric Unit 1
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select all 'ALA' residues (Alanines) in chain 'A'
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select residue range 5 to 10 in all chains
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select residue range 5 to 10 in chain 'A'
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Asym.Unit (74 KB)
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