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1DGG
Biol. Unit 1
Info
Asym.Unit (356 KB)
Biol.Unit 1 (349 KB)
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(1)
Title
:
HUMAN ERYTHROCYTE CATALSE CYANIDE COMPLEX
Authors
:
C. D. Putnam, A. S. Arvai, Y. Bourne, J. A. Tainer
Date
:
24 Nov 99 (Deposition) - 17 Feb 00 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.80
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B,C,D (1x)
Keywords
:
Catalase, Heme, Nadph, Hydrogen Peroxide, Cyanide, 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
(3, 10)
Info
All Hetero Components
1a: CYANIDE ION (CYNa)
1b: CYANIDE ION (CYNb)
1c: CYANIDE ION (CYNc)
1d: CYANIDE ION (CYNd)
2a: PROTOPORPHYRIN IX CONTAINING FE (HEMa)
2b: PROTOPORPHYRIN IX CONTAINING FE (HEMb)
2c: PROTOPORPHYRIN IX CONTAINING FE (HEMc)
2d: PROTOPORPHYRIN IX CONTAINING FE (HEMd)
3a: NADPH DIHYDRO-NICOTINAMIDE-ADENINE... (NDPa)
3b: NADPH DIHYDRO-NICOTINAMIDE-ADENINE... (NDPb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CYN
4
Ligand/Ion
CYANIDE ION
2
HEM
4
Ligand/Ion
PROTOPORPHYRIN IX CONTAINING FE
3
NDP
2
Ligand/Ion
NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDEPHOSPHATE
[
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Sites
(10, 10)
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)
View:
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Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
VAL A:74 , HIS A:75 , PHE A:161 , TYR A:358 , HEM A:2000
BINDING SITE FOR RESIDUE CYN A 4000
02
AC2
SOFTWARE
VAL B:74 , HIS B:75 , PHE B:161 , TYR B:358 , HEM B:2001 , HOH B:4055
BINDING SITE FOR RESIDUE CYN B 4001
03
AC3
SOFTWARE
VAL C:74 , HIS C:75 , PHE C:161 , TYR C:358 , HEM C:2002 , HOH C:4245
BINDING SITE FOR RESIDUE CYN C 4002
04
AC4
SOFTWARE
VAL D:74 , HIS D:75 , PHE D:161 , TYR D:358 , HEM D:2003
BINDING SITE FOR RESIDUE CYN D 4003
05
AC5
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 , GLY A:216 , SER A:217 , PHE A:334 , MET A:350 , ARG A:354 , TYR A:358 , THR A:361 , HIS A:362 , ARG A:365 , CYN A:4000 , HOH A:4142 , HOH A:4154 , HOH A:4186 , MET C:61 , ASP C:65
BINDING SITE FOR RESIDUE HEM A 2000
06
AC6
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:4027 , HOH A:4214 , HOH A:4218 , HOH A:4265 , HOH A:4278 , HOH A:4335 , HOH A:4365
BINDING SITE FOR RESIDUE NDP A 3000
07
AC7
SOFTWARE
ARG B:72 , VAL B:74 , HIS B:75 , ARG B:112 , GLY B:131 , VAL B:146 , GLY B:147 , ASN B:148 , PRO B:158 , PHE B:161 , GLY B:216 , SER B:217 , LEU B:299 , PHE B:334 , MET B:350 , ARG B:354 , TYR B:358 , HIS B:362 , ARG B:365 , CYN B:4001 , HOH B:4054 , HOH B:4066 , HOH B:4233
BINDING SITE FOR RESIDUE HEM B 2001
08
AC8
SOFTWARE
MET A:61 , ASP A:65 , 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 , PRO C:158 , PHE C:161 , GLY C:216 , SER C:217 , PHE C:334 , MET C:350 , ARG C:354 , TYR C:358 , THR C:361 , HIS C:362 , ARG C:365 , CYN C:4002 , HOH C:4058 , HOH C:4059 , HOH C:4141
BINDING SITE FOR RESIDUE HEM C 2002
09
AC9
SOFTWARE
HIS C:194 , PHE C:198 , SER C:201 , ARG C:203 , ASN C:213 , HIS C:235 , LYS C:237 , TRP C:303 , PRO C:304 , HIS C:305 , GLN C:442 , PHE C:446 , VAL C:450 , HOH C:4158 , HOH C:4176 , HOH C:4318
BINDING SITE FOR RESIDUE NDP C 3001
10
BC1
SOFTWARE
MET B:61 , ASP B:65 , ARG D:72 , VAL D:73 , VAL D:74 , HIS D:75 , ARG D:112 , GLY D:131 , VAL D:146 , GLY D:147 , ASN D:148 , PHE D:161 , GLY D:216 , SER D:217 , PHE D:334 , MET D:350 , ARG D:354 , ALA D:357 , TYR D:358 , THR D:361 , HIS D:362 , ARG D:365 , CYN D:4003 , HOH D:4022 , HOH D:4044 , HOH D:4139
BINDING SITE FOR RESIDUE HEM D 2003
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
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Sorry, no Info available
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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:
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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
[
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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.
(no "Exon" information available for biological units yet)
SCOP Domains
(1, 4)
Info
All SCOP Domains
1a: SCOP_d1dgga_ (A:)
1b: SCOP_d1dggb_ (B:)
1c: SCOP_d1dggc_ (C:)
1d: SCOP_d1dggd_ (D:)
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Protein Domains
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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
d1dgga_
A:
1b
d1dggb_
B:
1c
d1dggc_
C:
1d
d1dggd_
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)
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Sorry, no Info available
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Chain C
Chain D
Asymmetric Unit 1
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select chains 'A' and 'C'
select [ALA]:A
select all 'ALA' residues (Alanines) in chain 'A'
select 5-10
select residue range 5 to 10 in all chains
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select residue range 5 to 10 in chain 'A'
select protein & not helix & not sheet
select non-helix/non-sheet protein parts
set fontsize 20
set label size to 20 (allowed range: 1-58)
ssbonds 100
show SS bonds with a radius of 100 units (=0.4Å)
wireframe 100
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