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2VD7
Asym. Unit
Info
Asym.Unit (128 KB)
Biol.Unit 1 (62 KB)
Biol.Unit 2 (63 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF JMJD2A COMPLEXED WITH INHIBITOR PYRIDINE-2,4-DICARBOXYLIC ACID
Authors
:
S. S. Ng, F. Von Delft, E. S. Pilka, K. L. Kavanagh, M. A. Mcdonough, P. Sa C. H. Arrowsmith, J. Weigelt, A. Edwards, M. Sundstrom, C. J. Schofiel U. Oppermann
Date
:
01 Oct 07 (Deposition) - 27 Nov 07 (Release) - 11 Dec 13 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.25
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Keywords
:
Oxidoreductase, Phosphorylation, Chromatin Regulator, Iron, Nucleus, Zinc-Finger, Dioxygenase, Host-Virus Interaction, Transcription Regulation, Transcription, Metal-Binding, Histone Demethylation Inhibitor Jmjc Domain
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
N. R. Rose, S. S. Ng, J. Mecinovic, B. M. R. Lienard, S. H. Bello, Z. Sun, M. A. Mcdonough, U. Oppermann, C. J. Schofield
Inhibitor Scaffolds For 2-Oxoglutarate-Dependent Histone Lysine Demethylases.
J. Med. Chem. V. 51 7053 2008
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Hetero Components
(3, 6)
Info
All Hetero Components
1a: NICKEL (II) ION (NIa)
1b: NICKEL (II) ION (NIb)
2a: PYRIDINE-2,4-DICARBOXYLIC ACID (PD2a)
2b: PYRIDINE-2,4-DICARBOXYLIC ACID (PD2b)
3a: ZINC ION (ZNa)
3b: ZINC ION (ZNb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
NI
2
Ligand/Ion
NICKEL (II) ION
2
PD2
2
Ligand/Ion
PYRIDINE-2,4-DICARBOXYLIC ACID
3
ZN
2
Ligand/Ion
ZINC ION
[
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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
HIS A:188 , GLU A:190 , HIS A:276 , PD2 A:1356 , HOH A:2096
BINDING SITE FOR RESIDUE NI A 501
2
AC2
SOFTWARE
CYS A:234 , HIS A:240 , CYS A:306 , CYS A:308
BINDING SITE FOR RESIDUE ZN A 502
3
AC3
SOFTWARE
HIS B:188 , GLU B:190 , HIS B:276 , PD2 B:1356 , HOH B:2100
BINDING SITE FOR RESIDUE NI B 501
4
AC4
SOFTWARE
CYS B:234 , HIS B:240 , CYS B:306 , CYS B:308
BINDING SITE FOR RESIDUE ZN B 502
5
AC5
SOFTWARE
TYR A:132 , TYR A:177 , PHE A:185 , HIS A:188 , GLU A:190 , LYS A:206 , TRP A:208 , LYS A:241 , HIS A:276 , NI A:501 , HOH A:2091 , HOH A:2096 , HOH A:2121 , HOH A:2172
BINDING SITE FOR RESIDUE PD2 A1356
6
AC6
SOFTWARE
TYR B:132 , TYR B:177 , PHE B:185 , HIS B:188 , GLU B:190 , LYS B:206 , TRP B:208 , LYS B:241 , HIS B:276 , NI B:501 , HOH B:2091 , HOH B:2100 , HOH B:2132 , HOH B:2184 , HOH B:2185
BINDING SITE FOR RESIDUE PD2 B1356
[
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
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Label:
Sorry, no Info available
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PROSITE Patterns/Profiles
(2, 4)
Info
All PROSITE Patterns/Profiles
1: JMJN (A:14-56,B:14-56)
2: JMJC (A:142-308,B:142-308)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
JMJN
PS51183
JmjN domain profile.
KDM4A_HUMAN
14-56
2
A:14-56
B:14-56
2
JMJC
PS51184
JmjC domain profile.
KDM4A_HUMAN
142-308
2
A:142-308
B:142-308
[
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Exons
(8, 16)
Info
All Exons
Exon 1.3a (A:6-46 | B:7-46)
Exon 1.5 (A:47-105 | B:47-105)
Exon 1.6 (A:105-143 | B:105-143)
Exon 1.7 (A:144-208 | B:144-208)
Exon 1.8 (A:208-225 | B:208-225)
Exon 1.9b (A:225-259 | B:225-259)
Exon 1.10c (A:260-305 | B:260-305)
Exon 1.11 (A:306-355 | B:306-355)
View:
Select:
Label:
All Exon Boundaries
1: Boundary 1.1b/1.3a
2: Boundary 1.3a/1.5
3: Boundary 1.5/1.6
4: Boundary 1.6/1.7
5: Boundary 1.7/1.8
6: Boundary 1.8/1.9b
7: Boundary 1.9b/1.10c
8: Boundary 1.10c/1.11
9: Boundary 1.11/1.12
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
1.1b
ENST00000372396
1b
ENSE00001894244
chr1:
44115829-44115923
95
KDM4A_HUMAN
-
0
0
-
-
1.3a
ENST00000372396
3a
ENSE00002186574
chr1:
44118808-44118984
177
KDM4A_HUMAN
1-46
46
2
A:6-46
B:7-46
41
40
1.5
ENST00000372396
5
ENSE00001143140
chr1:
44121262-44121437
176
KDM4A_HUMAN
47-105
59
2
A:47-105
B:47-105
59
59
1.6
ENST00000372396
6
ENSE00000957378
chr1:
44125969-44126083
115
KDM4A_HUMAN
105-143
39
2
A:105-143
B:105-143
39
39
1.7
ENST00000372396
7
ENSE00000957379
chr1:
44128565-44128758
194
KDM4A_HUMAN
144-208
65
2
A:144-208
B:144-208
65
65
1.8
ENST00000372396
8
ENSE00000957380
chr1:
44131367-44131416
50
KDM4A_HUMAN
208-225
18
2
A:208-225
B:208-225
18
18
1.9b
ENST00000372396
9b
ENSE00001690958
chr1:
44132123-44132226
104
KDM4A_HUMAN
225-259
35
2
A:225-259
B:225-259
35
35
1.10c
ENST00000372396
10c
ENSE00000957382
chr1:
44132625-44132762
138
KDM4A_HUMAN
260-305
46
2
A:260-305
B:260-305
46
46
1.11
ENST00000372396
11
ENSE00000957383
chr1:
44133443-44133690
248
KDM4A_HUMAN
306-388
83
2
A:306-355
B:306-355
50
50
1.12
ENST00000372396
12
ENSE00000957384
chr1:
44134771-44134970
200
KDM4A_HUMAN
388-455
68
0
-
-
1.13b
ENST00000372396
13b
ENSE00000957385
chr1:
44137176-44137546
371
KDM4A_HUMAN
455-578
124
0
-
-
1.14
ENST00000372396
14
ENSE00001080538
chr1:
44149355-44149475
121
KDM4A_HUMAN
579-619
41
0
-
-
1.15
ENST00000372396
15
ENSE00000957387
chr1:
44154585-44154766
182
KDM4A_HUMAN
619-679
61
0
-
-
1.16b
ENST00000372396
16b
ENSE00001143055
chr1:
44156516-44156720
205
KDM4A_HUMAN
680-748
69
0
-
-
1.17
ENST00000372396
17
ENSE00001143047
chr1:
44157167-44157243
77
KDM4A_HUMAN
748-773
26
0
-
-
1.18b
ENST00000372396
18b
ENSE00001143039
chr1:
44157927-44157982
56
KDM4A_HUMAN
774-792
19
0
-
-
1.19
ENST00000372396
19
ENSE00001143030
chr1:
44159665-44159773
109
KDM4A_HUMAN
792-828
37
0
-
-
1.20
ENST00000372396
20
ENSE00001143023
chr1:
44160380-44160565
186
KDM4A_HUMAN
829-890
62
0
-
-
1.21
ENST00000372396
21
ENSE00001080535
chr1:
44163514-44163684
171
KDM4A_HUMAN
891-947
57
0
-
-
1.22a
ENST00000372396
22a
ENSE00001080539
chr1:
44169288-44169407
120
KDM4A_HUMAN
948-987
40
0
-
-
1.23
ENST00000372396
23
ENSE00001080536
chr1:
44169691-44169783
93
KDM4A_HUMAN
988-1018
31
0
-
-
1.24a
ENST00000372396
24a
ENSE00001841454
chr1:
44169901-44171186
1286
KDM4A_HUMAN
1019-1064
46
0
-
-
[
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SCOP Domains
(1, 2)
Info
All SCOP Domains
1a: SCOP_d2vd7a_ (A:)
1b: SCOP_d2vd7b_ (B:)
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Protein Domains
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Organisms
(
)
(
)
Class
:
All beta proteins
(24004)
Fold
:
Double-stranded beta-helix
(580)
Superfamily
:
Clavaminate synthase-like
(197)
Family
:
Histone demethylase core
(19)
Protein domain
:
JMJD2A core
(13)
Human (Homo sapiens) [TaxId: 9606]
(13)
1a
d2vd7a_
A:
1b
d2vd7b_
B:
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CATH Domains
(0, 0)
Info
all CATH domains
View:
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Sorry, no Info available
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Pfam Domains
(2, 4)
Info
all PFAM domains
1a: PFAM_JmjC_2vd7B01 (B:175-291)
1b: PFAM_JmjC_2vd7B02 (B:175-291)
2a: PFAM_JmjN_2vd7B03 (B:15-49)
2b: PFAM_JmjN_2vd7B04 (B:15-49)
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Clans
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(
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Organisms
(
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)
Clan
:
Cupin
(179)
Family
:
JmjC
(39)
Homo sapiens (Human)
(31)
1a
JmjC-2vd7B01
B:175-291
1b
JmjC-2vd7B02
B:175-291
Clan
:
no clan defined [family: JmjN]
(16)
Family
:
JmjN
(16)
Homo sapiens (Human)
(16)
2a
JmjN-2vd7B03
B:15-49
2b
JmjN-2vd7B04
B:15-49
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