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5FYB
Asym. Unit
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Asym.Unit (98 KB)
Biol.Unit 1 (90 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF HUMAN JARID1B IN COMPLEX WITH MC1648
Authors
:
R. Nowak, V. Srikannathasan, D. Rotili, C. Johansson, C. Gileadi, K. Ku C. Strain-Damerell, A. Szykowska, F. Von Delft, N. A. Burgess-Brown C. H. Arrowsmith, C. Bountra, A. M. Edwards, U. Oppermann
Date
:
05 Mar 16 (Deposition) - 29 Mar 17 (Release) - 29 Mar 17 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.87
Chains
:
Asym. Unit : A
Biol. Unit 1: A (1x)
Keywords
:
Oxidoreductase, Jarid1B, Plu1
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
R. Nowak, V. Srikannathasan, D. Rotili, C. Johansson, C. Gileadi, K. Kupinska, C. Strain-Damerell, A. Szykowska, F. Von Delft, N. A. Burgess-Brown, C. H. Arrowsmith, C. Bountra, A. M. Edwards, U. Oppermann
Crystal Structure Of The Catalytic Domain Of Human Jarid1B In Complex With Mc1648
To Be Published
[
close entry info
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Hetero Components
(5, 28)
Info
All Hetero Components
1a: N-HYDROXY-3-[(6-OXO-4-PHENYL-1,6-D... (77Ja)
1b: N-HYDROXY-3-[(6-OXO-4-PHENYL-1,6-D... (77Jb)
2a: DIMETHYL SULFOXIDE (DMSa)
2b: DIMETHYL SULFOXIDE (DMSb)
2c: DIMETHYL SULFOXIDE (DMSc)
2d: DIMETHYL SULFOXIDE (DMSd)
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)
4c: MANGANESE (II) ION (MNc)
4d: MANGANESE (II) ION (MNd)
5a: ZINC ION (ZNa)
5b: ZINC ION (ZNb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
77J
2
Ligand/Ion
N-HYDROXY-3-[(6-OXO-4-PHENYL-1,6-DIHYDROPYRIMIDIN-2-YL)SULFANYL]PROPANAMIDE
2
DMS
4
Ligand/Ion
DIMETHYL SULFOXIDE
3
EDO
16
Ligand/Ion
1,2-ETHANEDIOL
4
MN
4
Ligand/Ion
MANGANESE (II) ION
5
ZN
2
Ligand/Ion
ZINC ION
[
close Hetero Component info
]
Sites
(28, 28)
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)
27: CC9 (SOFTWARE)
28: DC1 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
CYS A:692 , CYS A:695 , CYS A:715 , HIS A:718
BINDING SITE FOR RESIDUE ZN A 1754
02
AC2
SOFTWARE
CYS A:706 , CYS A:708 , CYS A:723 , CYS A:725
BINDING SITE FOR RESIDUE ZN A 1755
03
AC3
SOFTWARE
HIS A:499 , GLU A:501 , HIS A:587 , 77J A:1761 , HOH A:2241
BINDING SITE FOR RESIDUE MN A 1756
04
AC4
SOFTWARE
HOH A:2432
BINDING SITE FOR RESIDUE MN A 1757
05
AC5
SOFTWARE
HIS A:399
BINDING SITE FOR RESIDUE MN A 1758
06
AC6
SOFTWARE
SER A:544
BINDING SITE FOR RESIDUE MN A 1759
07
AC7
SOFTWARE
GLU A:31 , CYS A:32 , PRO A:33 , VAL A:34 , ILE A:55 , HOH A:2014
BINDING SITE FOR RESIDUE 77J A 1760
08
AC8
SOFTWARE
TYR A:488 , PHE A:496 , HIS A:499 , GLU A:501 , SER A:507 , ASN A:509 , LYS A:517 , TRP A:519 , HIS A:587 , ASN A:591 , MN A:1756 , EDO A:1770 , DMS A:1780 , DMS A:1781 , HOH A:2233 , HOH A:2241
BINDING SITE FOR RESIDUE 77J A 1761
09
AC9
SOFTWARE
PHE A:83 , GLY A:426 , ALA A:427 , LEU A:487 , VAL A:489 , HOH A:2176
BINDING SITE FOR RESIDUE EDO A 1762
10
BC1
SOFTWARE
ARG A:666 , LEU A:732 , TYR A:734 , THR A:737 , HOH A:2377 , HOH A:2460
BINDING SITE FOR RESIDUE EDO A 1763
11
BC2
SOFTWARE
ARG A:612 , ASP A:630 , MET A:658 , GLU A:662 , EDO A:1776 , HOH A:2327
BINDING SITE FOR RESIDUE EDO A 1764
12
BC3
SOFTWARE
PRO A:30 , VAL A:568 , TYR A:569
BINDING SITE FOR RESIDUE EDO A 1765
13
BC4
SOFTWARE
ASP A:688 , GLU A:689 , ARG A:690 , GLN A:691 , VAL A:693 , GLY A:711 , LEU A:712 , LEU A:713
BINDING SITE FOR RESIDUE EDO A 1766
14
BC5
SOFTWARE
GLY A:524 , TYR A:525 , ARG A:584 , LEU A:610 , HOH A:2270 , HOH A:2463 , HOH A:2464
BINDING SITE FOR RESIDUE EDO A 1767
15
BC6
SOFTWARE
ARG A:670 , VAL A:674 , ILE A:675 , HOH A:2169 , HOH A:2376
BINDING SITE FOR RESIDUE EDO A 1768
16
BC7
SOFTWARE
HIS A:564
BINDING SITE FOR RESIDUE EDO A 1769
17
BC8
SOFTWARE
VAL A:99 , TRP A:486 , TYR A:488 , 77J A:1761 , DMS A:1781 , HOH A:2119 , HOH A:2224
BINDING SITE FOR RESIDUE EDO A 1770
18
BC9
SOFTWARE
ASP A:387 , ALA A:388 , VAL A:398 , HOH A:2129 , HOH A:2137 , HOH A:2465
BINDING SITE FOR RESIDUE EDO A 1771
19
CC1
SOFTWARE
LEU A:405 , LYS A:408 , GLU A:409 , ASP A:676 , HOH A:2005
BINDING SITE FOR RESIDUE EDO A 1772
20
CC2
SOFTWARE
GLU A:678 , LYS A:731 , ARG A:733 , HOH A:2438
BINDING SITE FOR RESIDUE EDO A 1773
21
CC3
SOFTWARE
MET A:680 , HOH A:2408 , HOH A:2466
BINDING SITE FOR RESIDUE EDO A 1774
22
CC4
SOFTWARE
PRO A:28 , PRO A:29 , PRO A:30 , MET A:562 , LEU A:750 , HOH A:2452
BINDING SITE FOR RESIDUE EDO A 1775
23
CC5
SOFTWARE
VAL A:615 , ARG A:619 , THR A:697 , EDO A:1764 , HOH A:2325 , HOH A:2430
BINDING SITE FOR RESIDUE EDO A 1776
24
CC6
SOFTWARE
LYS A:80 , GLU A:721 , CYS A:723 , SER A:724 , HOH A:2434
BINDING SITE FOR RESIDUE EDO A 1777
25
CC7
SOFTWARE
GLU A:631 , GLU A:683 , TYR A:736
BINDING SITE FOR RESIDUE DMS A 1778
26
CC8
SOFTWARE
ILE A:500 , TRP A:504 , HIS A:617 , TYR A:618 , LEU A:621 , ARG A:623 , HOH A:2245 , HOH A:2280 , HOH A:2340
BINDING SITE FOR RESIDUE DMS A 1779
27
CC9
SOFTWARE
GLN A:88 , GLN A:96 , THR A:97 , TYR A:425 , SER A:495 , PHE A:496 , CYS A:497 , 77J A:1761 , HOH A:2237
BINDING SITE FOR RESIDUE DMS A 1780
28
DC1
SOFTWARE
TRP A:486 , TYR A:488 , GLU A:501 , SER A:507 , ASN A:601 , 77J A:1761 , EDO A:1770
BINDING SITE FOR RESIDUE DMS A 1781
[
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]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
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Sorry, no Info available
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PROSITE Patterns/Profiles
(0, 0)
Info
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;
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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
(0, 0)
Info
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Sorry, no Info available
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CATH Domains
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Sorry, no Info available
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Pfam Domains
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Info
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Sorry, no Info available
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Asymmetric Unit 1
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select residue range 5 to 10 in all chains
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select non-helix/non-sheet protein parts
set fontsize 20
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