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5A7O
Asym. Unit
Info
Asym.Unit (131 KB)
Biol.Unit 1 (65 KB)
Biol.Unit 2 (65 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF HUMAN JMJD2A IN COMPLEX WITH COMPOUND 42
Authors
:
R. Nowak, S. Velupillai, T. Krojer, C. Gileadi, C. Johansson, M. Korczy D. D. Le, N. Younger, E. Gregori-Puigjane, A. Tumber, E. Iwasa, S. B. Po I. Ortiz Torres, D. M. Pinkas, F. Von Delft, C. H. Arrowsmith, C. Boun A. Edwards, B. K. Shoichet, D. G. Fujimori, U. Oppermann
Date
:
09 Jul 15 (Deposition) - 13 Jan 16 (Release) - 09 Mar 16 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.15
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Keywords
:
Oxidoreductase, Jmjd2A, Kdm4A
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
M. Korczynska, D. D. Le, N. Younger, E. Gregori-Puigjane, A. Tumber, T. Krojer, S. Velupillai, C. Gileadi, R. P. Nowak, E. Iwasa, S. B. Pollock, I. Ortiz Torres, U. Oppermann, B. K. Shoichet, D. G. Fujimori
Docking And Linking Of Fragments To Discover Jumonji Histone Demethylase Inhibitors.
J. Med. Chem. V. 59 1580 2016
[
close entry info
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Hetero Components
(6, 26)
Info
All Hetero Components
1a: 2-[5-(2-METHOXYETHANOYLAMINO)-2-OX... (7WHa)
1b: 2-[5-(2-METHOXYETHANOYLAMINO)-2-OX... (7WHb)
2a: DIMETHYL SULFOXIDE (DMSa)
2b: DIMETHYL SULFOXIDE (DMSb)
3a: 1,2-ETHANEDIOL (EDOa)
3b: 1,2-ETHANEDIOL (EDOb)
3c: 1,2-ETHANEDIOL (EDOc)
3d: 1,2-ETHANEDIOL (EDOd)
3e: 1,2-ETHANEDIOL (EDOe)
3f: 1,2-ETHANEDIOL (EDOf)
3g: 1,2-ETHANEDIOL (EDOg)
3h: 1,2-ETHANEDIOL (EDOh)
3i: 1,2-ETHANEDIOL (EDOi)
3j: 1,2-ETHANEDIOL (EDOj)
3k: 1,2-ETHANEDIOL (EDOk)
3l: 1,2-ETHANEDIOL (EDOl)
3m: 1,2-ETHANEDIOL (EDOm)
3n: 1,2-ETHANEDIOL (EDOn)
3o: 1,2-ETHANEDIOL (EDOo)
3p: 1,2-ETHANEDIOL (EDOp)
4a: MANGANESE (II) ION (MNa)
4b: MANGANESE (II) ION (MNb)
5a: SULFATE ION (SO4a)
5b: SULFATE ION (SO4b)
6a: ZINC ION (ZNa)
6b: ZINC ION (ZNb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
7WH
2
Ligand/Ion
2-[5-(2-METHOXYETHANOYLAMINO)-2-OXIDANYL-PHENYL]PYRIDINE-4-CARBOXYLIC ACID
2
DMS
2
Ligand/Ion
DIMETHYL SULFOXIDE
3
EDO
16
Ligand/Ion
1,2-ETHANEDIOL
4
MN
2
Ligand/Ion
MANGANESE (II) ION
5
SO4
2
Ligand/Ion
SULFATE ION
6
ZN
2
Ligand/Ion
ZINC ION
[
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Sites
(26, 26)
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)
11: BC2 (SOFTWARE)
12: BC3 (SOFTWARE)
13: BC4 (SOFTWARE)
14: BC5 (SOFTWARE)
15: BC6 (SOFTWARE)
16: BC7 (SOFTWARE)
17: BC8 (SOFTWARE)
18: BC9 (SOFTWARE)
19: CC1 (SOFTWARE)
20: CC2 (SOFTWARE)
21: CC3 (SOFTWARE)
22: CC4 (SOFTWARE)
23: CC5 (SOFTWARE)
24: CC6 (SOFTWARE)
25: CC7 (SOFTWARE)
26: CC8 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
PHE A:227 , PRO A:228 , GLY A:229 , SER A:230 , HOH A:2108 , HOH A:2109 , LYS B:105
BINDING SITE FOR RESIDUE SO4 A1355
02
AC2
SOFTWARE
LYS A:105 , PHE B:227 , PRO B:228 , GLY B:229 , SER B:230
BINDING SITE FOR RESIDUE SO4 B1355
03
AC3
SOFTWARE
TYR A:132 , PHE A:185 , HIS A:188 , GLU A:190 , ASN A:198 , LYS A:206 , TRP A:208 , LYS A:241 , HIS A:276 , MN A:1369 , DMS A:1370 , HOH A:2030 , HOH A:2086
BINDING SITE FOR RESIDUE 7WH A1356
04
AC4
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 , MN B:1363 , DMS B:1364 , HOH B:2066 , HOH B:2085
BINDING SITE FOR RESIDUE 7WH B1356
05
AC5
SOFTWARE
SER A:316 , MET A:317 , ASP A:318 , HOH A:2152 , HOH A:2172
BINDING SITE FOR RESIDUE EDO A1357
06
AC6
SOFTWARE
LYS A:224 , GLU A:235 , ALA A:236 , PHE A:237 , LEU A:238 , EDO A:1367 , HOH A:2112
BINDING SITE FOR RESIDUE EDO A1358
07
AC7
SOFTWARE
LYS B:224 , GLU B:235 , ALA B:236 , PHE B:237 , LEU B:238 , HOH B:2103 , HOH B:2116
BINDING SITE FOR RESIDUE EDO B1357
08
AC8
SOFTWARE
GLN B:73 , LEU B:74 , VAL B:75 , LEU B:125 , THR B:126 , PHE B:127 , PRO B:129 , PRO B:130
BINDING SITE FOR RESIDUE EDO B1358
09
AC9
SOFTWARE
ARG A:98
BINDING SITE FOR RESIDUE EDO A1359
10
BC1
SOFTWARE
LEU A:81 , PHE A:82 , THR A:83 , PHE A:227 , HOH B:2061
BINDING SITE FOR RESIDUE EDO A1360
11
BC2
SOFTWARE
LYS A:217 , TYR A:273 , GLN A:302 , VAL A:304 , HOH A:2089
BINDING SITE FOR RESIDUE EDO A1361
12
BC3
SOFTWARE
GLN A:78 , SER A:79 , TRP A:122 , LYS A:123 , HOH A:2027 , HOH A:2050
BINDING SITE FOR RESIDUE EDO A1362
13
BC4
SOFTWARE
ARG B:25 , PHE B:27 , ASP B:146 , TRP B:148 , ASN B:149
BINDING SITE FOR RESIDUE EDO B1359
14
BC5
SOFTWARE
GLY A:138 , THR A:139
BINDING SITE FOR RESIDUE EDO A1363
15
BC6
SOFTWARE
GLU A:23 , ARG A:29 , HOH A:2010
BINDING SITE FOR RESIDUE EDO A1364
16
BC7
SOFTWARE
LYS B:217 , GLN B:302 , HOH B:2088
BINDING SITE FOR RESIDUE EDO B1360
17
BC8
SOFTWARE
MET A:312 , VAL A:313 , LYS A:314
BINDING SITE FOR RESIDUE EDO A1365
18
BC9
SOFTWARE
LYS A:89 , LYS A:90
BINDING SITE FOR RESIDUE EDO A1366
19
CC1
SOFTWARE
HIS A:188 , THR A:189 , LEU A:238 , ARG A:239 , TYR A:275 , EDO A:1358
BINDING SITE FOR RESIDUE EDO A1367
20
CC2
SOFTWARE
ARG B:98
BINDING SITE FOR RESIDUE EDO B1361
21
CC3
SOFTWARE
CYS A:234 , HIS A:240 , CYS A:306 , CYS A:308
BINDING SITE FOR RESIDUE ZN A1368
22
CC4
SOFTWARE
CYS B:234 , HIS B:240 , CYS B:306 , CYS B:308
BINDING SITE FOR RESIDUE ZN B1362
23
CC5
SOFTWARE
HIS A:188 , GLU A:190 , HIS A:276 , 7WH A:1356 , HOH A:2086
BINDING SITE FOR RESIDUE MN A1369
24
CC6
SOFTWARE
HIS B:188 , GLU B:190 , HIS B:276 , 7WH B:1356 , HOH B:2085
BINDING SITE FOR RESIDUE MN B1363
25
CC7
SOFTWARE
GLY A:170 , TYR A:177 , GLU A:190 , SER A:288 , 7WH A:1356
BINDING SITE FOR RESIDUE DMS A1370
26
CC8
SOFTWARE
GLY B:170 , TYR B:175 , TYR B:177 , GLU B:190 , SER B:288 , ASN B:290 , 7WH B:1356
BINDING SITE FOR RESIDUE DMS B1364
[
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
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PROSITE Patterns/Profiles
(0, 0)
Info
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;
View:
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End label:
Sorry, no Info available
[
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Exons
(0, 0)
Info
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Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
SCOP Domains
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Info
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CATH Domains
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all CATH domains
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Sorry, no Info available
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Pfam Domains
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Asymmetric Unit 1
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select all 'ALA' residues (Alanines) in chain 'A'
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select residue range 5 to 10 in all chains
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select residue range 5 to 10 in chain 'A'
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select non-helix/non-sheet protein parts
set fontsize 20
set label size to 20 (allowed range: 1-58)
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wireframe 100
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In this "Basic Interface" any change in the selection of a pulldown menu automatically triggers an action (one-step mechanism).
View and selection are coupled in the structure specific controls (e.g. "Hetero","PROSITE") .
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Asym.Unit (131 KB)
Header - Asym.Unit
Biol.Unit 1 (65 KB)
Header - Biol.Unit 1
Biol.Unit 2 (65 KB)
Header - Biol.Unit 2
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