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2IUW
Asym. Unit
Info
Asym.Unit (87 KB)
Biol.Unit 1 (162 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF HUMAN ABH3 IN COMPLEX WITH IRON ION AND 2-OXOGLUTARATE
Authors
:
O. Sundheim, C. B. Vagbo, M. Bjoras, M. M. L. Desousa, V. Talstad, P. A. Aas, F. Drablos, H. E. Krokan, J. A. Tainer, G. Slupphaug
Date
:
07 Jun 06 (Deposition) - 26 Jul 06 (Release) - 22 Dec 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.50
Chains
:
Asym. Unit : A
Biol. Unit 1: A (2x)
Keywords
:
Oxidoreductase, Dna/Rna Repair, Demethylase, Beta Jellyroll
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
O. Sundheim, C. B. Vagbo, M. Bjoras, M. M. L. Desousa, V. Talstad, P. A. Aas, F. Drablos, H. E. Krokan, J. A. Tainer, G. Slupphaug
Human Abh3 Structure And Key Residues For Oxidative Demethylation To Reverse Dna/Rna Damage.
Embo J. V. 25 3389 2006
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Hetero Components
(4, 9)
Info
All Hetero Components
1a: 2-OXOGLUTARIC ACID (AKGa)
2a: BETA-MERCAPTOETHANOL (BMEa)
2b: BETA-MERCAPTOETHANOL (BMEb)
2c: BETA-MERCAPTOETHANOL (BMEc)
2d: BETA-MERCAPTOETHANOL (BMEd)
3a: FE (III) ION (FEa)
3b: FE (III) ION (FEb)
3c: FE (III) ION (FEc)
4a: (4R)-5-OXO-L-LEUCINE (LEDa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
AKG
1
Ligand/Ion
2-OXOGLUTARIC ACID
2
BME
4
Ligand/Ion
BETA-MERCAPTOETHANOL
3
FE
3
Ligand/Ion
FE (III) ION
4
LED
1
Mod. Amino Acid
(4R)-5-OXO-L-LEUCINE
[
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Sites
(8, 8)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
6: AC6 (SOFTWARE)
7: AC7 (SOFTWARE)
8: AC8 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
HIS A:191 , ASP A:193 , HIS A:257 , AKG A:700 , HOH A:2150
BINDING SITE FOR RESIDUE FE A 500
2
AC2
SOFTWARE
ARG A:74 , GLU A:75 , HOH A:2006
BINDING SITE FOR RESIDUE FE A 501
3
AC3
SOFTWARE
SER A:81 , SER A:83 , GLY A:86 , SER A:88 , ASP A:254
BINDING SITE FOR RESIDUE FE A 502
4
AC4
SOFTWARE
LED A:177 , ASN A:179 , TYR A:181 , HIS A:191 , ASP A:193 , HIS A:257 , VAL A:259 , ARG A:269 , ASN A:271 , ARG A:275 , FE A:500 , HOH A:2150 , HOH A:2225 , HOH A:2226
BINDING SITE FOR RESIDUE AKG A 700
5
AC5
SOFTWARE
CYS A:91 , GLU A:248
BINDING SITE FOR RESIDUE BME A 800
6
AC6
SOFTWARE
THR A:85 , GLU A:166 , GLU A:167 , CYS A:201 , HOH A:2118
BINDING SITE FOR RESIDUE BME A 801
7
AC7
SOFTWARE
CYS A:110 , PRO A:268 , HOH A:2227
BINDING SITE FOR RESIDUE BME A 802
8
AC8
SOFTWARE
ASP A:189 , ARG A:258 , PRO A:260 , LYS A:261 , HOH A:2043
BINDING SITE FOR RESIDUE BME A 901
[
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SAPs(SNPs)/Variants
(1, 1)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_026632 (R164C, chain A, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_026632
R
164
C
ALKB3_HUMAN
Polymorphism
2271815
A
R
164
C
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
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PROSITE Patterns/Profiles
(1, 1)
Info
All PROSITE Patterns/Profiles
1: FE2OG_OXY (A:172-278)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
FE2OG_OXY
PS51471
Fe(2+) 2-oxoglutarate dioxygenase domain profile.
ALKB3_HUMAN
172-278
1
A:172-278
[
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Exons
(8, 8)
Info
All Exons
Exon 1.3d (A:67-70)
Exon 1.4 (A:71-73)
Exon 1.5a (A:73-89)
Exon 1.6a (A:89-124)
Exon 1.7 (A:124-153)
Exon 1.10c (A:154-222)
Exon 1.11c (A:231-256)
Exon 1.12c (A:257-279)
View:
Select:
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All Exon Boundaries
1: Boundary 1.2c/1.3d
2: Boundary 1.3d/1.4
3: Boundary 1.4/1.5a
4: Boundary 1.5a/1.6a
5: Boundary 1.6a/1.7
6: Boundary 1.7/1.10c
7: Boundary 1.10c/1.11c
8: Boundary 1.11c/1.12c
9: Boundary 1.12c/-
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
1.1d
ENST00000302708
1d
ENSE00002194114
chr11:
43902389-43902729
341
ALKB3_HUMAN
-
0
0
-
-
1.2c
ENST00000302708
2c
ENSE00001248417
chr11:
43904133-43904281
149
ALKB3_HUMAN
1-27
27
0
-
-
1.3d
ENST00000302708
3d
ENSE00001136406
chr11:
43904635-43904738
104
ALKB3_HUMAN
27-61
35
1
A:67-70
4
1.4
ENST00000302708
4
ENSE00001100883
chr11:
43905533-43905567
35
ALKB3_HUMAN
62-73
12
1
A:71-73
3
1.5a
ENST00000302708
5a
ENSE00001182888
chr11:
43908156-43908203
48
ALKB3_HUMAN
73-89
17
1
A:73-89
17
1.6a
ENST00000302708
6a
ENSE00001182884
chr11:
43911275-43911378
104
ALKB3_HUMAN
89-124
36
1
A:89-124
36
1.7
ENST00000302708
7
ENSE00001182880
chr11:
43913591-43913679
89
ALKB3_HUMAN
124-153
30
1
A:124-153
30
1.10c
ENST00000302708
10c
ENSE00001100880
chr11:
43923066-43923275
210
ALKB3_HUMAN
154-223
70
1
A:154-222
69
1.11c
ENST00000302708
11c
ENSE00001100892
chr11:
43940588-43940686
99
ALKB3_HUMAN
224-256
33
1
A:231-256
26
1.12c
ENST00000302708
12c
ENSE00002191074
chr11:
43941468-43941762
295
ALKB3_HUMAN
257-286
30
1
A:257-279
23
[
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SCOP Domains
(1, 1)
Info
All SCOP Domains
1a: SCOP_d2iuwa1 (A:70-279)
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(
)
Class
:
All beta proteins
(24004)
Fold
:
Double-stranded beta-helix
(580)
Superfamily
:
Clavaminate synthase-like
(197)
Family
:
AlkB-like
(29)
Protein domain
:
AlkB homolog 3
(1)
Human (Homo sapiens) [TaxId: 9606]
(1)
1a
d2iuwa1
A:70-279
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CATH Domains
(0, 0)
Info
all CATH domains
View:
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Label:
Sorry, no Info available
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Pfam Domains
(0, 0)
Info
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Label:
Sorry, no Info available
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Chain A
Asymmetric Unit 1
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