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3THP
Asym. Unit
Info
Asym.Unit (56 KB)
Biol.Unit 1 (51 KB)
Biol.Unit 2 (196 KB)
Biol.Unit 3 (99 KB)
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(1)
Title
:
CRYSTAL STRUCTURE AND RNA BINDING PROPERTIES OF THE RRM/ALKB DOMAINS IN HUMAN ABH8, AN ENZYME CATALYZING TRNA HYPERMODIFICATION, NORTHEAST STRUCTURAL GENOMICS CONSORTIUM TARGET HR5601B
Authors
:
C. Pastore, I. Topalidou, F. Forouhar, A. C. Yan, M. Levy, J. F. Hunt, Nor Structural Genomics Consortium (Nesg)
Date
:
19 Aug 11 (Deposition) - 02 Nov 11 (Release) - 10 Oct 12 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
3.20
Chains
:
Asym. Unit : A
Biol. Unit 1: A (1x)
Biol. Unit 2: A (4x)
Biol. Unit 3: A (2x)
Keywords
:
Structural Genomics, Psi-Biology, Northeast Structural Genomics Consortium, Nesg, Alpha-Beta Two Domain-Protein Containing A Zinc Structure Motif, Trna Modifying Enzyme, Oxidoreductase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
C. Pastore, I. Topalidou, F. Forouhar, A. C. Yan, M. Levy, J. F. Hunt
Crystal Structure And Rna Binding Properties Of The Rna Recognition Motif (Rrm) And Alkb Domains In Human Alkb Homolog 8 (Abh8), An Enzyme Catalyzing Trna Hypermodification.
J. Biol. Chem. V. 287 2130 2012
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Hetero Components
(4, 10)
Info
All Hetero Components
1a: 2-OXOGLUTARIC ACID (AKGa)
2a: MANGANESE (II) ION (MNa)
3a: SELENOMETHIONINE (MSEa)
3b: SELENOMETHIONINE (MSEb)
3c: SELENOMETHIONINE (MSEc)
3d: SELENOMETHIONINE (MSEd)
3e: SELENOMETHIONINE (MSEe)
3f: SELENOMETHIONINE (MSEf)
3g: SELENOMETHIONINE (MSEg)
4a: ZINC ION (ZNa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
AKG
1
Ligand/Ion
2-OXOGLUTARIC ACID
2
MN
1
Ligand/Ion
MANGANESE (II) ION
3
MSE
7
Mod. Amino Acid
SELENOMETHIONINE
4
ZN
1
Ligand/Ion
ZINC ION
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Sites
(3, 3)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
HIS A:242 , CYS A:341 , CYS A:343 , CYS A:349
BINDING SITE FOR RESIDUE ZN A 401
2
AC2
SOFTWARE
HIS A:238 , ASP A:240 , HIS A:292 , AKG A:403
BINDING SITE FOR RESIDUE MN A 402
3
AC3
SOFTWARE
ASN A:227 , TYR A:229 , HIS A:238 , SER A:251 , MSE A:260 , HIS A:292 , ARG A:328 , SER A:330 , THR A:332 , ARG A:334 , MN A:402
BINDING SITE FOR RESIDUE AKG A 403
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
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Sorry, no Info available
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PROSITE Patterns/Profiles
(1, 1)
Info
All PROSITE Patterns/Profiles
1: FE2OG_OXY (A:220-337)
;
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End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
FE2OG_OXY
PS51471
Fe(2+) 2-oxoglutarate dioxygenase domain profile.
ALKB8_HUMAN
220-337
1
A:220-337
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Exons
(9, 9)
Info
All Exons
Exon 1.6 (A:28-43)
Exon 1.7 (A:44-123)
Exon 1.8a (A:123-156)
Exon 1.9 (A:174-199 (gaps))
Exon 1.10b (A:199-234)
Exon 1.11 (A:234-257)
Exon 1.12b (A:258-293)
Exon 1.13 (A:293-344 (gaps))
Exon 1.14 (A:344-360 (gaps))
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All Exon Boundaries
01: Boundary 1.5/1.6
02: Boundary 1.6/1.7
03: Boundary 1.7/1.8a
04: Boundary 1.8a/1.9
05: Boundary 1.9/1.10b
06: Boundary 1.10b/1.11
07: Boundary 1.11/1.12b
08: Boundary 1.12b/1.13
09: Boundary 1.13/1.14
10: Boundary 1.14/1.15
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
1.2
ENST00000389568
2
ENSE00001724312
chr11:
107436244-107436179
66
ALKB8_HUMAN
-
0
0
-
-
1.3
ENST00000389568
3
ENSE00001620533
chr11:
107435940-107435888
53
ALKB8_HUMAN
-
0
0
-
-
1.4
ENST00000389568
4
ENSE00001769102
chr11:
107434462-107434273
190
ALKB8_HUMAN
-
0
0
-
-
1.5
ENST00000389568
5
ENSE00001727109
chr11:
107433542-107433425
118
ALKB8_HUMAN
-
0
0
-
-
1.6
ENST00000389568
6
ENSE00002152837
chr11:
107431625-107431491
135
ALKB8_HUMAN
1-43
43
1
A:28-43
16
1.7
ENST00000389568
7
ENSE00000990040
chr11:
107427729-107427492
238
ALKB8_HUMAN
44-123
80
1
A:44-123
80
1.8a
ENST00000389568
8a
ENSE00000930433
chr11:
107424704-107424573
132
ALKB8_HUMAN
123-167
45
1
A:123-156
34
1.9
ENST00000389568
9
ENSE00000930432
chr11:
107423929-107423834
96
ALKB8_HUMAN
167-199
33
1
A:174-199 (gaps)
26
1.10b
ENST00000389568
10b
ENSE00000930431
chr11:
107422638-107422534
105
ALKB8_HUMAN
199-234
36
1
A:199-234
36
1.11
ENST00000389568
11
ENSE00001506233
chr11:
107420549-107420479
71
ALKB8_HUMAN
234-257
24
1
A:234-257
24
1.12b
ENST00000389568
12b
ENSE00001687648
chr11:
107403132-107403026
107
ALKB8_HUMAN
258-293
36
1
A:258-293
36
1.13
ENST00000389568
13
ENSE00001697189
chr11:
107396318-107396167
152
ALKB8_HUMAN
293-344
52
1
A:293-344 (gaps)
52
1.14
ENST00000389568
14
ENSE00001611673
chr11:
107393281-107393025
257
ALKB8_HUMAN
344-429
86
1
A:344-360 (gaps)
33
1.15
ENST00000389568
15
ENSE00001634419
chr11:
107381762-107381613
150
ALKB8_HUMAN
430-479
50
0
-
-
1.16c
ENST00000389568
16c
ENSE00001763825
chr11:
107375941-107375321
621
ALKB8_HUMAN
480-664
185
0
-
-
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SCOP Domains
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Pfam Domains
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Asym.Unit (56 KB)
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