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5FYS
Asym. Unit
Info
Asym.Unit (96 KB)
Biol.Unit 1 (88 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF HUMAN JARID1B IN COMPLEX WITH D-2-HYDROXYGLUTARATE
Authors
:
R. Nowak, J. Kopec, C. Johansson, C. Gileadi, K. Kupinska, C. Strain-Da A. Szykowska, F. Von Delft, N. A. Burgess-Brown, C. H. Arrowsmith, C. A. M. Edwards, U. Oppermann
Date
:
09 Mar 16 (Deposition) - 22 Mar 17 (Release) - 22 Mar 17 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.89
Chains
:
Asym. Unit : A
Biol. Unit 1: A (1x)
Keywords
:
Oxidoreductase, Jarid1B, Plu1, Tca Intermediate
(Keyword Search:
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Gene Ontology, PubMed, Web (Google)
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)
Reference
:
R. Nowak, J. Kopec, 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 D-2-Hydroxyglutarate
To Be Published
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Hetero Components
(6, 21)
Info
All Hetero Components
1a: (2R)-2-HYDROXYPENTANEDIOIC ACID (2HGa)
2a: CHLORIDE ION (CLa)
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)
4a: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ET... (EPEa)
5a: MANGANESE (II) ION (MNa)
5b: MANGANESE (II) ION (MNb)
6a: ZINC ION (ZNa)
6b: ZINC ION (ZNb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
2HG
1
Ligand/Ion
(2R)-2-HYDROXYPENTANEDIOIC ACID
2
CL
1
Ligand/Ion
CHLORIDE ION
3
EDO
14
Ligand/Ion
1,2-ETHANEDIOL
4
EPE
1
Ligand/Ion
4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
5
MN
2
Ligand/Ion
MANGANESE (II) ION
6
ZN
2
Ligand/Ion
ZINC ION
[
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Sites
(21, 21)
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)
View:
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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 , 2HG A:1773 , HOH A:2089
BINDING SITE FOR RESIDUE MN A 1756
04
AC4
SOFTWARE
HIS A:718
BINDING SITE FOR RESIDUE MN A 1757
05
AC5
SOFTWARE
TRP A:504 , MET A:534 , LEU A:541 , LEU A:552 , ARG A:584 , TYR A:586 , HIS A:617 , TYR A:618 , LEU A:621 , ARG A:623 , HOH A:2170 , HOH A:2175 , HOH A:2324
BINDING SITE FOR RESIDUE EPE A 1758
06
AC6
SOFTWARE
ASP A:630 , CYS A:699 , PHE A:700 , MET A:701 , SER A:702 , HOH A:2244
BINDING SITE FOR RESIDUE EDO A 1759
07
AC7
SOFTWARE
GLY A:426 , ALA A:427 , ASP A:428 , PHE A:434 , LEU A:487 , TYR A:488 , VAL A:489
BINDING SITE FOR RESIDUE EDO A 1760
08
AC8
SOFTWARE
ARG A:666 , TYR A:734 , THR A:737 , HOH A:2326
BINDING SITE FOR RESIDUE EDO A 1761
09
AC9
SOFTWARE
ARG A:612 , ASP A:630 , MET A:658 , GLU A:662 , HOH A:2229
BINDING SITE FOR RESIDUE EDO A 1762
10
BC1
SOFTWARE
PRO A:30 , VAL A:568
BINDING SITE FOR RESIDUE EDO A 1763
11
BC2
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 1764
12
BC3
SOFTWARE
GLY A:524 , TYR A:525 , HOH A:2195 , HOH A:2327
BINDING SITE FOR RESIDUE EDO A 1765
13
BC4
SOFTWARE
ARG A:670 , VAL A:674 , ILE A:675 , HOH A:2134 , HOH A:2267
BINDING SITE FOR RESIDUE EDO A 1766
14
BC5
SOFTWARE
TYR A:425 , SER A:494 , SER A:495 , ASN A:591 , 2HG A:1773 , HOH A:2138 , HOH A:2189
BINDING SITE FOR RESIDUE EDO A 1767
15
BC6
SOFTWARE
HIS A:564
BINDING SITE FOR RESIDUE EDO A 1768
16
BC7
SOFTWARE
TRP A:486 , TYR A:488 , ALA A:599 , ASN A:601 , 2HG A:1773 , HOH A:2089
BINDING SITE FOR RESIDUE EDO A 1769
17
BC8
SOFTWARE
ASP A:376
BINDING SITE FOR RESIDUE EDO A 1770
18
BC9
SOFTWARE
GLU A:36 , ARG A:65 , PRO A:66 , PRO A:68
BINDING SITE FOR RESIDUE EDO A 1771
19
CC1
SOFTWARE
HIS A:50
BINDING SITE FOR RESIDUE EDO A 1772
20
CC2
SOFTWARE
TYR A:488 , PHE A:496 , HIS A:499 , GLU A:501 , SER A:507 , ASN A:509 , TRP A:519 , HIS A:587 , ALA A:599 , MN A:1756 , EDO A:1767 , EDO A:1769 , HOH A:2087 , HOH A:2089
BINDING SITE FOR RESIDUE 2HG A 1773
21
CC3
SOFTWARE
LEU A:90 , ASN A:91 , LEU A:413 , THR A:416 , GLU A:419 , HOH A:2072
BINDING SITE FOR RESIDUE CL A 1774
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
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Exons
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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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Chain A
Asymmetric Unit 1
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Asym.Unit (96 KB)
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