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1QPA
Asym. Unit
Info
Asym.Unit (127 KB)
Biol.Unit 1 (119 KB)
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(1)
Title
:
LIGNIN PEROXIDASE ISOZYME LIP4.65 (PI 4.65)
Authors
:
T. H. Choinowski, K. Piontek
Date
:
08 Oct 96 (Deposition) - 11 Jan 97 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.80
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Keywords
:
Oxidoreductase, Lignin Degradation, Heme, Glycoprotein
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
T. Choinowski, W. Blodig, K. H. Winterhalter, K. Piontek
The Crystal Structure Of Lignin Peroxidase At 1. 70 A Resolution Reveals A Hydroxy Group On The Cbeta Of Tryptophan 171: A Novel Radical Site Formed During The Redo Cycle.
J. Mol. Biol. V. 286 809 1999
(for further references see the
PDB file header
)
[
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Hetero Components
(6, 19)
Info
All Hetero Components
1a: CALCIUM ION (CAa)
1b: CALCIUM ION (CAb)
1c: CALCIUM ION (CAc)
1d: CALCIUM ION (CAd)
2a: ALPHA-L-FUCOSE (FUCa)
3a: PROTOPORPHYRIN IX CONTAINING FE (HEMa)
3b: PROTOPORPHYRIN IX CONTAINING FE (HEMb)
4a: BETA-HYDROXYTRYPTOPHANE (HTRa)
4b: BETA-HYDROXYTRYPTOPHANE (HTRb)
5a: ALPHA-D-MANNOSE (MANa)
5b: ALPHA-D-MANNOSE (MANb)
5c: ALPHA-D-MANNOSE (MANc)
5d: ALPHA-D-MANNOSE (MANd)
5e: ALPHA-D-MANNOSE (MANe)
5f: ALPHA-D-MANNOSE (MANf)
5g: ALPHA-D-MANNOSE (MANg)
6a: N-ACETYL-D-GLUCOSAMINE (NAGa)
6b: N-ACETYL-D-GLUCOSAMINE (NAGb)
6c: N-ACETYL-D-GLUCOSAMINE (NAGc)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CA
4
Ligand/Ion
CALCIUM ION
2
FUC
1
Ligand/Ion
ALPHA-L-FUCOSE
3
HEM
2
Ligand/Ion
PROTOPORPHYRIN IX CONTAINING FE
4
HTR
2
Mod. Amino Acid
BETA-HYDROXYTRYPTOPHANE
5
MAN
7
Ligand/Ion
ALPHA-D-MANNOSE
6
NAG
3
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
[
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]
Sites
(18, 18)
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: HE3 (UNKNOWN)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ASN A:257 , LYS A:260 , HOH A:852 , GLY B:5
BINDING SITE FOR RESIDUE NAG A 360
02
AC2
SOFTWARE
SER A:334 , VAL A:335 , HOH A:473 , HOH A:475
BINDING SITE FOR RESIDUE MAN A 370
03
AC3
SOFTWARE
PRO A:228 , LEU A:229 , LYS A:230 , LYS A:308 , SER A:332 , ALA A:333 , HOH A:469
BINDING SITE FOR RESIDUE MAN A 375
04
AC4
SOFTWARE
ASN B:257 , LYS B:260 , NAG B:361 , FUC B:365
BINDING SITE FOR RESIDUE NAG B 360
05
AC5
SOFTWARE
NAG B:360
BINDING SITE FOR RESIDUE NAG B 361
06
AC6
SOFTWARE
GLU B:250 , SER B:253 , LYS B:260 , NAG B:360 , MAN B:380 , HOH B:582 , HOH B:591
BINDING SITE FOR RESIDUE FUC B 365
07
AC7
SOFTWARE
HOH A:440 , SER B:334 , VAL B:335 , ALA B:336 , HOH B:524 , HOH B:526
BINDING SITE FOR RESIDUE MAN B 370
08
AC8
SOFTWARE
PRO B:228 , LEU B:229 , LYS B:230 , LYS B:308 , SER B:332 , ALA B:333 , HOH B:520
BINDING SITE FOR RESIDUE MAN B 375
09
AC9
SOFTWARE
CYS B:317 , SER B:319 , THR B:320 , FUC B:365 , HOH B:589 , HOH B:592
BINDING SITE FOR RESIDUE MAN B 380
10
BC1
SOFTWARE
HIS B:310 , THR B:324 , MAN B:386
BINDING SITE FOR RESIDUE MAN B 385
11
BC2
SOFTWARE
ASN B:11 , ILE B:283 , HIS B:310 , ALA B:311 , MAN B:385
BINDING SITE FOR RESIDUE MAN B 386
12
BC3
SOFTWARE
SER A:177 , ASP A:194 , THR A:196 , GLN A:199 , ASP A:201
BINDING SITE FOR RESIDUE CA A 351
13
BC4
SOFTWARE
ASP A:48 , GLY A:66 , ASP A:68 , SER A:70 , HOH A:709 , HOH A:710
BINDING SITE FOR RESIDUE CA A 352
14
BC5
SOFTWARE
SER B:177 , ASP B:194 , THR B:196 , GLN B:199 , ASP B:201
BINDING SITE FOR RESIDUE CA B 351
15
BC6
SOFTWARE
ASP B:48 , GLY B:66 , ASP B:68 , SER B:70 , HOH B:404 , HOH B:405
BINDING SITE FOR RESIDUE CA B 352
16
BC7
SOFTWARE
HIS A:39 , GLU A:40 , ARG A:43 , PHE A:46 , ILE A:85 , GLU A:146 , PRO A:147 , LEU A:172 , LEU A:173 , ALA A:175 , HIS A:176 , ALA A:179 , ALA A:180 , ALA A:181 , ASN A:182 , ASP A:183 , VAL A:184 , LEU A:235 , THR A:237 , HOH A:398 , HOH A:755 , HOH A:757 , HOH A:758 , HOH A:779
BINDING SITE FOR RESIDUE HEM A 350
17
BC8
SOFTWARE
HIS B:39 , GLU B:40 , ARG B:43 , PHE B:46 , ILE B:85 , GLU B:146 , PRO B:147 , LEU B:172 , LEU B:173 , ALA B:175 , HIS B:176 , ALA B:179 , ALA B:180 , ALA B:181 , ASN B:182 , ASP B:183 , VAL B:184 , LEU B:235 , THR B:237 , HOH B:399 , HOH B:419 , HOH B:421 , HOH B:423
BINDING SITE FOR RESIDUE HEM B 350
18
HE3
UNKNOWN
HEM A:350 , HEM B:350
HEM 350
[
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
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PROSITE Patterns/Profiles
(2, 4)
Info
All PROSITE Patterns/Profiles
1: PEROXIDASE_2 (A:38-49,B:38-49)
2: PEROXIDASE_1 (A:168-178,B:168-178)
;
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.
LIG4_PHACH
67-78
2
A:38-49
B:38-49
2
PEROXIDASE_1
PS00435
Peroxidases proximal heme-ligand signature.
LIG4_PHACH
197-207
2
A:168-178
B:168-178
[
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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_d1qpaa_ (A:)
1b: SCOP_d1qpab_ (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)
Basidomycetes fungus (Phanerochaete chrysosporium) [TaxId: 5306]
(9)
1a
d1qpaa_
A:
1b
d1qpab_
B:
[
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CATH Domains
(2, 4)
Info
all CATH domains
1a: CATH_1qpaA01 (A:11-144,A:269-296)
1b: CATH_1qpaB01 (B:11-144,B:269-296)
2a: CATH_1qpaA02 (A:145-268,A:298-339)
2b: CATH_1qpaB02 (B:145-268,B:298-339)
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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. Strain: bkm-f1267.
(2)
1a
1qpaA01
A:11-144,A:269-296
1b
1qpaB01
B:11-144,B:269-296
Topology
:
Peroxidase; domain 2
(241)
Homologous Superfamily
:
Peroxidase, domain 2
(241)
Phanerochaete chrysosporium. Organism_taxid: 5306. Strain: bkm-f1267.
(2)
2a
1qpaA02
A:145-268,A:298-339
2b
1qpaB02
B:145-268,B:298-339
[
close CATH info
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Pfam Domains
(2, 4)
Info
all PFAM domains
1a: PFAM_DUF3415_1qpaB01 (B:259-341)
1b: PFAM_DUF3415_1qpaB02 (B:259-341)
2a: PFAM_peroxidase_1qpaB03 (B:20-257)
2b: PFAM_peroxidase_1qpaB04 (B:20-257)
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(
)
Organisms
(
)
(
)
Clan
:
no clan defined [family: DUF3415]
(12)
Family
:
DUF3415
(12)
Phanerochaete chrysosporium (White-rot fungus) (Sporotrichum pruinosum)
(7)
1a
DUF3415-1qpaB01
B:259-341
1b
DUF3415-1qpaB02
B:259-341
Clan
:
no clan defined [family: peroxidase]
(92)
Family
:
peroxidase
(92)
Phanerochaete chrysosporium (White-rot fungus) (Sporotrichum pruinosum)
(7)
2a
peroxidase-1qpaB03
B:20-257
2b
peroxidase-1qpaB04
B:20-257
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