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4HON
Biol. Unit 1
Info
Asym.Unit (129 KB)
Biol.Unit 1 (64 KB)
Biol.Unit 2 (62 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF HUMAN JMJD2D/KDM4D IN COMPLEX WITH AN H3K9ME3 PEPTIDE AND 2-OXOGLUTARATE
Authors
:
S. Krishnan, R. C. Trievel
Date
:
22 Oct 12 (Deposition) - 21 Nov 12 (Release) - 30 Jan 13 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.80
Chains
:
Asym. Unit : A,B,F,G
Biol. Unit 1: A,F (1x)
Biol. Unit 2: B,G (1x)
Keywords
:
Jumonji C Demethylase, Jmjd2/Kdm4 Family, Beta Barrel Fold, Oxidoreductase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
S. Krishnan, R. C. Trievel
Structural And Functional Analysis Of Jmjd2D Reveals Molecular Basis For Site-Specific Demethylation Among Jmjd2 Demethylases.
Structure V. 21 98 2013
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Hetero Components
(5, 17)
Info
All Hetero Components
1a: 2-OXOGLUTARIC ACID (AKGa)
1b: 2-OXOGLUTARIC ACID (AKGb)
2a: N-TRIMETHYLLYSINE (M3La)
2b: N-TRIMETHYLLYSINE (M3Lb)
3a: NICKEL (II) ION (NIa)
3b: NICKEL (II) ION (NIb)
4a: NITRATE ION (NO3a)
4b: NITRATE ION (NO3b)
4c: NITRATE ION (NO3c)
4d: NITRATE ION (NO3d)
4e: NITRATE ION (NO3e)
4f: NITRATE ION (NO3f)
4g: NITRATE ION (NO3g)
4h: NITRATE ION (NO3h)
4i: NITRATE ION (NO3i)
4j: NITRATE ION (NO3j)
4k: NITRATE ION (NO3k)
4l: NITRATE ION (NO3l)
5a: 1,3-PROPANDIOL (PDOa)
5b: 1,3-PROPANDIOL (PDOb)
5c: 1,3-PROPANDIOL (PDOc)
5d: 1,3-PROPANDIOL (PDOd)
5e: 1,3-PROPANDIOL (PDOe)
6a: THIOCYANATE ION (SCNa)
6b: THIOCYANATE ION (SCNb)
6c: THIOCYANATE ION (SCNc)
6d: THIOCYANATE ION (SCNd)
6e: THIOCYANATE ION (SCNe)
6f: THIOCYANATE ION (SCNf)
7a: ZINC ION (ZNa)
7b: ZINC ION (ZNb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
AKG
1
Ligand/Ion
2-OXOGLUTARIC ACID
2
M3L
1
Mod. Amino Acid
N-TRIMETHYLLYSINE
3
NI
-1
Ligand/Ion
NICKEL (II) ION
4
NO3
8
Ligand/Ion
NITRATE ION
5
PDO
4
Ligand/Ion
1,3-PROPANDIOL
6
SCN
3
Ligand/Ion
THIOCYANATE ION
7
ZN
-1
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: CC6 (SOFTWARE)
20: CC8 (SOFTWARE)
21: CC9 (SOFTWARE)
View:
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No.
Name
Evidence
Residues
Description
01
AC1
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 , PDO A:415 , HOH A:507 , M3L F:9 , HOH F:101
BINDING SITE FOR RESIDUE AKG A 401
02
AC2
SOFTWARE
HIS A:192 , GLU A:194 , HIS A:280 , AKG A:401 , HOH A:507
BINDING SITE FOR RESIDUE NI A 402
03
AC3
SOFTWARE
CYS A:238 , HIS A:244 , CYS A:310 , CYS A:312
BINDING SITE FOR RESIDUE ZN A 403
04
AC4
SOFTWARE
LYS A:150 , GLN A:151 , SCN A:406
BINDING SITE FOR RESIDUE SCN A 404
05
AC5
SOFTWARE
GLU A:27
BINDING SITE FOR RESIDUE SCN A 405
06
AC6
SOFTWARE
LYS A:58 , THR A:149 , SCN A:404
BINDING SITE FOR RESIDUE SCN A 406
07
AC7
SOFTWARE
GLU A:224 , ALA A:240 , PHE A:241 , LEU A:242 , HOH A:664 , HOH A:683
BINDING SITE FOR RESIDUE NO3 A 407
08
AC8
SOFTWARE
LYS A:305 , ARG A:332 , LEU A:335 , TRP A:336 , HOH A:549 , ASP B:302 , MET B:306
BINDING SITE FOR RESIDUE NO3 A 408
09
AC9
SOFTWARE
LYS A:305 , MET A:321 , TRP A:336 , GLN A:340 , HOH A:630 , HOH A:652
BINDING SITE FOR RESIDUE NO3 A 409
10
BC1
SOFTWARE
ASP A:302 , MET A:306 , HOH A:602 , HOH A:697 , LYS B:305 , ARG B:332 , LEU B:335 , TRP B:336
BINDING SITE FOR RESIDUE NO3 A 410
11
BC2
SOFTWARE
GLU A:314 , ALA A:315 , ARG A:316 , VAL A:317 , ALA F:7 , ARG F:8
BINDING SITE FOR RESIDUE NO3 A 411
12
BC3
SOFTWARE
PRO A:113 , LYS A:124 , ASN A:128 , TRP A:185 , LYS A:186 , HOH A:510
BINDING SITE FOR RESIDUE NO3 A 412
13
BC4
SOFTWARE
HOH A:720
BINDING SITE FOR RESIDUE NO3 A 413
14
BC5
SOFTWARE
SER A:67 , VAL A:98 , GLY A:99 , ARG A:102
BINDING SITE FOR RESIDUE NO3 A 414
15
BC6
SOFTWARE
PHE A:189 , ALA A:190 , HIS A:192 , LYS A:245 , AKG A:401 , HOH A:507 , HOH A:537 , SER F:10 , THR F:11 , HOH F:101
BINDING SITE FOR RESIDUE PDO A 415
16
BC7
SOFTWARE
THR A:87 , TYR A:89 , PHE A:231 , PRO A:232 , HOH A:536 , HOH A:561
BINDING SITE FOR RESIDUE PDO A 416
17
BC8
SOFTWARE
GLY A:142 , SER A:143
BINDING SITE FOR RESIDUE PDO A 417
18
BC9
SOFTWARE
MET A:19 , ILE A:20 , ILE B:20 , PHE B:21 , HIS B:22 , TYR B:34 , HOH B:570
BINDING SITE FOR RESIDUE PDO A 418
19
CC6
SOFTWARE
GLU A:68 , LYS B:124 , ASN B:128 , HOH B:576
BINDING SITE FOR RESIDUE SCN B 406
20
CC8
SOFTWARE
PRO A:217 , GLU A:218 , TYR A:277 , TYR A:303 , HOH A:625 , ASP B:334 , LEU B:335 , ARG B:338
BINDING SITE FOR RESIDUE NO3 B 408
21
CC9
SOFTWARE
ASP A:334 , LEU A:335 , ARG A:338 , PRO B:217 , GLU B:218 , TYR B:277 , TYR B:303 , HOH B:594
BINDING SITE FOR RESIDUE NO3 B 409
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
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PROSITE Patterns/Profiles
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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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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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set fontsize 20
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Asym.Unit (129 KB)
Header - Asym.Unit
Biol.Unit 1 (64 KB)
Header - Biol.Unit 1
Biol.Unit 2 (62 KB)
Header - Biol.Unit 2
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