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1DGB
Asym. Unit
Info
Asym.Unit (352 KB)
Biol.Unit 1 (345 KB)
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(1)
Title
:
HUMAN ERYTHROCYTE CATALASE
Authors
:
C. D. Putnam, A. S. Arvai, Y. Bourne, J. A. Tainer
Date
:
23 Nov 99 (Deposition) - 11 Feb 00 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.20
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B,C,D (1x)
Keywords
:
Catalase, Heme, Nadph, Hydrogen Peroxide, Oxidoreductase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
C. D. Putnam, A. S. Arvai, Y. Bourne, J. A. Tainer
Active And Inhibited Human Catalase Structures: Ligand And Nadph Binding And Catalytic Mechanism.
J. Mol. Biol. V. 296 295 2000
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(2, 6)
Info
All Hetero Components
1a: PROTOPORPHYRIN IX CONTAINING FE (HEMa)
1b: PROTOPORPHYRIN IX CONTAINING FE (HEMb)
1c: PROTOPORPHYRIN IX CONTAINING FE (HEMc)
1d: PROTOPORPHYRIN IX CONTAINING FE (HEMd)
2a: NADPH DIHYDRO-NICOTINAMIDE-ADENINE... (NDPa)
2b: NADPH DIHYDRO-NICOTINAMIDE-ADENINE... (NDPb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
HEM
4
Ligand/Ion
PROTOPORPHYRIN IX CONTAINING FE
2
NDP
2
Ligand/Ion
NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDEPHOSPHATE
[
close Hetero Component info
]
Sites
(6, 6)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
6: AC6 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
ARG A:72 , VAL A:73 , VAL A:74 , HIS A:75 , ARG A:112 , GLY A:131 , VAL A:146 , GLY A:147 , ASN A:148 , PHE A:161 , SER A:217 , PHE A:334 , MET A:350 , ARG A:354 , TYR A:358 , THR A:361 , HIS A:362 , ARG A:365 , HOH A:1450 , HOH A:1509 , HOH A:1522 , MET C:61
BINDING SITE FOR RESIDUE HEM A 1200
2
AC2
SOFTWARE
HIS A:194 , PHE A:198 , SER A:201 , ARG A:203 , ASN A:213 , HIS A:235 , LYS A:237 , VAL A:302 , TRP A:303 , PRO A:304 , HIS A:305 , GLN A:442 , PHE A:446 , VAL A:450 , HOH A:1385 , HOH A:1446 , HOH A:1484 , HOH A:1533 , HOH A:1557 , HOH A:1586 , HOH A:1605
BINDING SITE FOR RESIDUE NDP A 1300
3
AC3
SOFTWARE
ARG B:72 , VAL B:73 , VAL B:74 , HIS B:75 , ARG B:112 , GLY B:131 , VAL B:146 , GLY B:147 , ASN B:148 , PHE B:161 , SER B:217 , HIS B:218 , PHE B:334 , MET B:350 , ARG B:354 , TYR B:358 , THR B:361 , HIS B:362 , ARG B:365 , HOH B:1206 , HOH B:1215 , HOH B:1242
BINDING SITE FOR RESIDUE HEM B 1201
4
AC4
SOFTWARE
ARG C:72 , VAL C:73 , VAL C:74 , HIS C:75 , ARG C:112 , GLY C:131 , VAL C:146 , GLY C:147 , ASN C:148 , PHE C:161 , GLY C:216 , SER C:217 , PHE C:334 , MET C:350 , ARG C:354 , TYR C:358 , HIS C:362 , ARG C:365 , HOH C:1307 , HOH C:1328 , HOH C:1475 , HOH C:1497
BINDING SITE FOR RESIDUE HEM C 1202
5
AC5
SOFTWARE
HIS C:194 , PHE C:198 , SER C:201 , ARG C:203 , ASN C:213 , LYS C:237 , VAL C:302 , TRP C:303 , PRO C:304 , HIS C:305 , GLN C:442 , PHE C:446 , VAL C:450 , HOH C:1345 , HOH C:1431 , HOH C:1435 , HOH C:1483
BINDING SITE FOR RESIDUE NDP C 1301
6
AC6
SOFTWARE
ARG D:72 , VAL D:74 , HIS D:75 , ARG D:112 , GLY D:131 , VAL D:146 , GLY D:147 , ASN D:148 , PHE D:161 , SER D:217 , PHE D:334 , MET D:350 , ARG D:354 , TYR D:358 , THR D:361 , HIS D:362 , ARG D:365 , HOH D:1217 , HOH D:1223 , HOH D:1242 , HOH D:1381
BINDING SITE FOR RESIDUE HEM D 1203
[
close Site info
]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(3, 12)
Info
All PROSITE Patterns/Profiles
1: CATALASE_3 (A:24-501,B:24-501,C:24-501,D:24-50...)
2: CATALASE_2 (A:64-80,B:64-80,C:64-80,D:64-80)
3: CATALASE_1 (A:354-362,B:354-362,C:354-362,D:35...)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
CATALASE_3
PS51402
catalase family profile.
CATA_HUMAN
24-503
4
A:24-501
B:24-501
C:24-501
D:24-501
2
CATALASE_2
PS00438
Catalase proximal active site signature.
CATA_HUMAN
64-80
4
A:64-80
B:64-80
C:64-80
D:64-80
3
CATALASE_1
PS00437
Catalase proximal heme-ligand signature.
CATA_HUMAN
354-362
4
A:354-362
B:354-362
C:354-362
D:354-362
[
close PROSITE info
]
Exons
(12, 48)
Info
All Exons
Exon 1.1 (A:4-22 | B:4-22 | C:4-22 | D:5-22)
Exon 1.2 (A:23-80 | B:23-80 | C:23-80 | D:23...)
Exon 1.3 (A:80-117 | B:80-117 | C:80-117 | D...)
Exon 1.4 (A:117-160 | B:117-160 | C:117-160 ...)
Exon 1.5 (A:161-195 | B:161-195 | C:161-195 ...)
Exon 1.6 (A:196-237 | B:196-237 | C:196-237 ...)
Exon 1.7a (A:238-301 | B:238-301 | C:238-301 ...)
Exon 1.8a (A:302-352 | B:302-352 | C:302-352 ...)
Exon 1.9c (A:353-399 | B:353-399 | C:353-399 ...)
Exon 1.10b (A:399-442 | B:399-442 | C:399-442 ...)
Exon 1.11a (A:443-478 | B:443-478 | C:443-478 ...)
Exon 1.12b (A:479-501 | B:479-501 | C:479-501 ...)
View:
Select:
Label:
All Exon Boundaries
01: Boundary -/1.1
02: Boundary 1.1/1.2
03: Boundary 1.2/1.3
04: Boundary 1.3/1.4
05: Boundary 1.4/1.5
06: Boundary 1.5/1.6
07: Boundary 1.6/1.7a
08: Boundary 1.7a/1.8a
09: Boundary 1.8a/1.9c
10: Boundary 1.9c/1.10b
11: Boundary 1.10b/1.11a
12: Boundary 1.11a/1.12b
13: Boundary 1.12b/1.13b
View:
Label:
Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
ENSEMBL
UniProtKB
PDB
No.
Transcript ID
Exon
Exon ID
Genome Location
Length
ID
Location
Length
Count
Location
Length
1.1
ENST00000241052
1
ENSE00001004251
chr11:
34460472-34460626
155
CATA_HUMAN
1-22
22
4
A:4-22
B:4-22
C:4-22
D:5-22
19
19
19
18
1.2
ENST00000241052
2
ENSE00000824423
chr11:
34470739-34470910
172
CATA_HUMAN
23-80
58
4
A:23-80
B:23-80
C:23-80
D:23-80
58
58
58
58
1.3
ENST00000241052
3
ENSE00000824424
chr11:
34472535-34472645
111
CATA_HUMAN
80-117
38
4
A:80-117
B:80-117
C:80-117
D:80-117
38
38
38
38
1.4
ENST00000241052
4
ENSE00000824425
chr11:
34473624-34473754
131
CATA_HUMAN
117-160
44
4
A:117-160
B:117-160
C:117-160
D:117-160
44
44
44
44
1.5
ENST00000241052
5
ENSE00000824426
chr11:
34474637-34474741
105
CATA_HUMAN
161-195
35
4
A:161-195
B:161-195
C:161-195
D:161-195
35
35
35
35
1.6
ENST00000241052
6
ENSE00000824427
chr11:
34475348-34475473
126
CATA_HUMAN
196-237
42
4
A:196-237
B:196-237
C:196-237
D:196-237
42
42
42
42
1.7a
ENST00000241052
7a
ENSE00000824428
chr11:
34477558-34477749
192
CATA_HUMAN
238-301
64
4
A:238-301
B:238-301
C:238-301
D:238-301
64
64
64
64
1.8a
ENST00000241052
8a
ENSE00000824429
chr11:
34478212-34478364
153
CATA_HUMAN
302-352
51
4
A:302-352
B:302-352
C:302-352
D:302-352
51
51
51
51
1.9c
ENST00000241052
9c
ENSE00000824430
chr11:
34482798-34482936
139
CATA_HUMAN
353-399
47
4
A:353-399
B:353-399
C:353-399
D:353-399
47
47
47
47
1.10b
ENST00000241052
10b
ENSE00000824431
chr11:
34485652-34485782
131
CATA_HUMAN
399-442
44
4
A:399-442
B:399-442
C:399-442
D:399-442
44
44
44
44
1.11a
ENST00000241052
11a
ENSE00000824432
chr11:
34489835-34489942
108
CATA_HUMAN
443-478
36
4
A:443-478
B:443-478
C:443-478
D:443-478
36
36
36
36
1.12b
ENST00000241052
12b
ENSE00000824433
chr11:
34492505-34492588
84
CATA_HUMAN
479-506
28
4
A:479-501
B:479-501
C:479-501
D:479-501
23
23
23
23
1.13b
ENST00000241052
13b
ENSE00001004250
chr11:
34492915-34493609
695
CATA_HUMAN
507-527
21
0
-
-
[
close EXON info
]
SCOP Domains
(1, 4)
Info
All SCOP Domains
1a: SCOP_d1dgba_ (A:)
1b: SCOP_d1dgbb_ (B:)
1c: SCOP_d1dgbc_ (C:)
1d: SCOP_d1dgbd_ (D:)
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Protein Domains
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(
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Organisms
(
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(
)
Class
:
Multi-domain proteins (alpha and beta)
(2421)
Fold
:
Heme-dependent catalase-like
(82)
Superfamily
:
Heme-dependent catalase-like
(82)
Family
:
Heme-dependent catalases
(80)
Protein domain
:
Catalase I
(32)
Human (Homo sapiens) [TaxId: 9606]
(6)
1a
d1dgba_
A:
1b
d1dgbb_
B:
1c
d1dgbc_
C:
1d
d1dgbd_
D:
[
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CATH Domains
(0, 0)
Info
all CATH domains
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Sorry, no Info available
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Pfam Domains
(0, 0)
Info
all PFAM domains
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Sorry, no Info available
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Chain D
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Asym.Unit (352 KB)
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