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1VGI
Asym. Unit
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Asym.Unit (43 KB)
Biol.Unit 1 (39 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF XENON BOUND RAT HEME-HEME OXYGENASE-1 COMPLEX
Authors
:
M. Sugishima, H. Sakamoto, M. Noguchi, K. Fukuyama
Date
:
26 Apr 04 (Deposition) - 31 Aug 04 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.90
Chains
:
Asym. Unit : A
Biol. Unit 1: A (1x)
Keywords
:
Hydrophobic Cavity, Xenon Binding, Oxidoreductase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
M. Sugishima, H. Sakamoto, M. Noguchi, K. Fukuyama
Co-Trapping Site In Heme Oxygenase Revealed By Photolysis Of Its Co-Bound Heme Complex: Mechanism Of Escaping From Product Inhibition
J. Mol. Biol. V. 341 7 2004
(for further references see the
PDB file header
)
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Hetero Components
(3, 3)
Info
All Hetero Components
1a: FORMIC ACID (FMTa)
2a: PROTOPORPHYRIN IX CONTAINING FE (HEMa)
3a: XENON (XEa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
FMT
1
Ligand/Ion
FORMIC ACID
2
HEM
1
Ligand/Ion
PROTOPORPHYRIN IX CONTAINING FE
3
XE
1
Ligand/Ion
XENON
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Sites
(3, 3)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
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No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
LYS A:18 , HIS A:25 , GLU A:29 , MET A:34 , TYR A:134 , THR A:135 , ARG A:136 , GLY A:139 , SER A:142 , GLY A:143 , VAL A:146 , LEU A:147 , LYS A:179 , ARG A:183 , PHE A:207 , PHE A:214 , HOH A:323 , HOH A:369
BINDING SITE FOR RESIDUE HEM A 300
2
AC2
SOFTWARE
PHE A:37
BINDING SITE FOR RESIDUE XE A 301
3
AC3
SOFTWARE
ARG A:27 , ILE A:211 , HOH A:350
BINDING SITE FOR RESIDUE FMT A 302
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
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PROSITE Patterns/Profiles
(1, 1)
Info
All PROSITE Patterns/Profiles
1: HEME_OXYGENASE (A:129-139)
;
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End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
HEME_OXYGENASE
PS00593
Heme oxygenase signature.
HMOX1_RAT
129-139
1
A:129-139
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Exons
(3, 3)
Info
All Exons
Exon 1.2 (A:11-48)
Exon 1.3b (A:49-212)
Exon 1.4 (A:213-222)
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All Exon Boundaries
1: Boundary 1.1/1.2
2: Boundary 1.2/1.3b
3: Boundary 1.3b/1.4
4: Boundary 1.4/1.5a
View:
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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
ENSRNOT00000019192
1
ENSRNOE00000437660
chr19:
13963139-13963277
139
HMOX1_RAT
1-8
8
0
-
-
1.2
ENSRNOT00000019192
2
ENSRNOE00000433615
chr19:
13965179-13965299
121
HMOX1_RAT
8-48
41
1
A:11-48
38
1.3b
ENSRNOT00000019192
3b
ENSRNOE00000135098
chr19:
13966126-13966617
492
HMOX1_RAT
49-212
164
1
A:49-212
164
1.4
ENSRNOT00000019192
4
ENSRNOE00000135373
chr19:
13968127-13968226
100
HMOX1_RAT
213-246
34
1
A:213-222
10
1.5a
ENSRNOT00000019192
5a
ENSRNOE00000265745
chr19:
13969266-13969955
690
HMOX1_RAT
246-289
44
0
-
-
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SCOP Domains
(1, 1)
Info
All SCOP Domains
1a: SCOP_d1vgia_ (A:)
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(
)
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)
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)
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(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
Heme oxygenase-like
(107)
Superfamily
:
Heme oxygenase-like
(107)
Family
:
Eukaryotic type heme oxygenase
(69)
Protein domain
:
Heme oxygenase-1 (HO-1)
(49)
Norway rat (Rattus norvegicus) [TaxId: 10116]
(25)
1a
d1vgia_
A:
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CATH Domains
(1, 1)
Info
all CATH domains
1a: CATH_1vgiA00 (A:11-222)
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)
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)
Homologous Superfamilies
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)
(
)
Organisms
(
)
(
)
Class
:
Mainly Alpha
(13335)
Architecture
:
Up-down Bundle
(3216)
Topology
:
Heme Oxygenase; Chain A
(84)
Homologous Superfamily
:
Heme Oxygenase; Chain A
(84)
Norway rat (Rattus norvegicus)
(13)
1a
1vgiA00
A:11-222
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Pfam Domains
(1, 1)
Info
all PFAM domains
1a: PFAM_Heme_oxygenase_1vgiA01 (A:11-216)
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Clans
(
)
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(
)
Organisms
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)
(
)
Clan
:
HO
(49)
Family
:
Heme_oxygenase
(37)
Rattus norvegicus (Rat)
(4)
1a
Heme_oxygenase-1vgiA01
A:11-216
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Asymmetric Unit 1
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