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5PMY
Asym. Unit
Info
Asym.Unit (77 KB)
Biol.Unit 1 (70 KB)
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(1)
Title
:
PANDDA ANALYSIS GROUP DEPOSITION -- CRYSTAL STRUCTURE OF JMJD2D AFTER INITIAL REFINEMENT WITH NO LIGAND MODELLED (STRUCTURE 192)
Authors
:
N. M. Pearce, T. Krojer, R. Talon, A. R. Bradley, M. Fairhead, R. Sethi, N E. Maclean, P. Collins, J. Brandao-Neto, A. Douangamath, Z. Renjie, A M. Vollmar, J. Ng, A. Szykowska, N. Burgess-Brown, P. E. Brennan, O. Co U. Oppermann, C. Bountra, C. H. Arrowsmith, A. Edwards, F. Von Delft
Date
:
07 Feb 17 (Deposition) - 15 Mar 17 (Release) - 15 Mar 17 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.29
Chains
:
Asym. Unit : A
Biol. Unit 1: A (1x)
Keywords
:
Pandda, Sgc - Diamond I04-1 Fragment Screening, Jmj Domain, Epigenetics, Oxidoreductase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
N. M. Pearce, T. Krojer, A. R. Bradley, P. Collins, R. Nowak, R. Talon, B. Marsden, S. Kelm, J. Shi, D. Deane, F. Von Delft
Pandda Analysis Group Deposition
To Be Published
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Hetero Components
(6, 15)
Info
All Hetero Components
1a: 1,2-ETHANEDIOL (EDOa)
1b: 1,2-ETHANEDIOL (EDOb)
1c: 1,2-ETHANEDIOL (EDOc)
1d: 1,2-ETHANEDIOL (EDOd)
1e: 1,2-ETHANEDIOL (EDOe)
1f: 1,2-ETHANEDIOL (EDOf)
1g: 1,2-ETHANEDIOL (EDOg)
1h: 1,2-ETHANEDIOL (EDOh)
2a: MAGNESIUM ION (MGa)
3a: NICKEL (II) ION (NIa)
4a: N-OXALYLGLYCINE (OGAa)
5a: SULFATE ION (SO4a)
5b: SULFATE ION (SO4b)
5c: SULFATE ION (SO4c)
6a: ZINC ION (ZNa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
EDO
8
Ligand/Ion
1,2-ETHANEDIOL
2
MG
1
Ligand/Ion
MAGNESIUM ION
3
NI
1
Ligand/Ion
NICKEL (II) ION
4
OGA
1
Ligand/Ion
N-OXALYLGLYCINE
5
SO4
3
Ligand/Ion
SULFATE ION
6
ZN
1
Ligand/Ion
ZINC ION
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Sites
(15, 15)
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: AD1 (SOFTWARE)
11: AD2 (SOFTWARE)
12: AD3 (SOFTWARE)
13: AD4 (SOFTWARE)
14: AD5 (SOFTWARE)
15: AD6 (SOFTWARE)
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No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
CYS A:238 , HIS A:244 , CYS A:310 , CYS A:312
binding site for residue ZN A 401
02
AC2
SOFTWARE
HIS A:192 , GLU A:194 , HIS A:280 , OGA A:404 , HOH A:585
binding site for residue NI A 402
03
AC3
SOFTWARE
ASN A:65 , ILE A:66 , SER A:67 , GLU A:68 , ILE A:69 , VAL A:171
binding site for residue MG A 403
04
AC4
SOFTWARE
TYR A:136 , PHE A:189 , HIS A:192 , GLU A:194 , SER A:200 , ASN A:202 , LYS A:210 , TRP A:212 , HIS A:280 , NI A:402 , EDO A:412 , HOH A:585 , HOH A:638
binding site for residue OGA A 404
05
AC5
SOFTWARE
LYS A:150 , GLN A:151 , TRP A:152 , ASN A:153 , HIS A:156 , HOH A:642 , HOH A:781
binding site for residue EDO A 405
06
AC6
SOFTWARE
THR A:252 , ARG A:263 , HOH A:591
binding site for residue EDO A 406
07
AC7
SOFTWARE
GLU A:224 , ALA A:240 , PHE A:241 , LEU A:242 , TYR A:279 , SER A:308 , HOH A:508 , HOH A:524
binding site for residue EDO A 407
08
AC8
SOFTWARE
ASP A:64 , ASN A:65 , ILE A:66 , SER A:67 , GLU A:68 , ARG A:82 , HOH A:513
binding site for residue EDO A 408
09
AC9
SOFTWARE
PHE A:118 , ILE A:264 , THR A:265 , HOH A:563
binding site for residue EDO A 409
10
AD1
SOFTWARE
TRP A:57 , LYS A:58 , ALA A:59 , ARG A:60 , TYR A:63 , TYR A:203 , HOH A:505 , HOH A:520 , HOH A:595 , HOH A:670
binding site for residue EDO A 410
11
AD2
SOFTWARE
SER A:80 , THR A:87 , CYS A:168 , LYS A:305 , HOH A:532 , HOH A:567
binding site for residue EDO A 411
12
AD3
SOFTWARE
TYR A:181 , SER A:200 , ALA A:292 , ASN A:294 , OGA A:404 , HOH A:585
binding site for residue EDO A 412
13
AD4
SOFTWARE
ARG A:102 , HIS A:103 , ASN A:106 , HOH A:512 , HOH A:559 , HOH A:667
binding site for residue SO4 A 413
14
AD5
SOFTWARE
ARG A:60 , GLU A:61 , THR A:62 , ASN A:65 , HOH A:506 , HOH A:539 , HOH A:542 , HOH A:776
binding site for residue SO4 A 414
15
AD6
SOFTWARE
ARG A:123 , LYS A:124 , LYS A:127 , ASN A:128
binding site for residue SO4 A 415
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SAPs(SNPs)/Variants
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Exons
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SCOP Domains
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CATH Domains
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Pfam Domains
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Chain A
Asymmetric Unit 1
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