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5LY2
Asym. Unit
Info
Asym.Unit (257 KB)
Biol.Unit 1 (248 KB)
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(1)
Title
:
JMJD2A/ KDM4A COMPLEXED WITH NI(II), NOG AND MACROCYCLIC PEPTIDE INHIBITOR CP2_R6KME3 (13-MER)
Authors
:
R. Chowdhury, S. K. Madden, R. Hopkinson, C. J. Schofield
Date
:
23 Sep 16 (Deposition) - 12 Apr 17 (Release) - 19 Apr 17 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.43
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H
Biol. Unit 1: A,B,C,D,E,F,G,H (1x)
Keywords
:
Jmjd2A, Kdm4A, Oxidoreductase, Non-Heme, Iron, 2-Oxoglutarate, Dioxygenase, Oxygenase, Double-Stranded Beta Helix, Dsbh, Facial Triad, Demethylase, Histone, Jmjc Domain, Metal Binding Protein, Epigenetic And Transcription Regulation, Chromatin Regulator, Hydroxylation
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
A. Kawamura, M. Munzel, T. Kojima, C. Yapp, B. Bhushan, Y. Goto, A. Tumber, T. Katoh, O. N. King, T. Passioura, L. J. Walport, S. B. Hatch S. Madden, S. Muller, P. E. Brennan, R. Chowdhury, R. J. Hopkinson, H. Suga, C. J. Schofield
Highly Selective Inhibition Of Histone Demethylases By De Novo Macrocyclic Peptides.
Nat Commun V. 8 14773 2017
(for further references see the
PDB file header
)
[
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Hetero Components
(8, 30)
Info
All Hetero Components
1a: {[(2R)-2,3-DIAMINO-3-OXOPROPYL]SUL... (48Va)
1b: {[(2R)-2,3-DIAMINO-3-OXOPROPYL]SUL... (48Vb)
2a: CHLORIDE ION (CLa)
2b: CHLORIDE ION (CLb)
2c: CHLORIDE ION (CLc)
2d: CHLORIDE ION (CLd)
2e: CHLORIDE ION (CLe)
3a: D-TYROSINE (DTYa)
3b: D-TYROSINE (DTYb)
4a: GLYCEROL (GOLa)
4b: GLYCEROL (GOLb)
4c: GLYCEROL (GOLc)
4d: GLYCEROL (GOLd)
4e: GLYCEROL (GOLe)
5a: N-TRIMETHYLLYSINE (M3La)
5b: N-TRIMETHYLLYSINE (M3Lb)
5c: N-TRIMETHYLLYSINE (M3Lc)
5d: N-TRIMETHYLLYSINE (M3Ld)
6a: NICKEL (II) ION (NIa)
6b: NICKEL (II) ION (NIb)
6c: NICKEL (II) ION (NIc)
6d: NICKEL (II) ION (NId)
7a: N-OXALYLGLYCINE (OGAa)
7b: N-OXALYLGLYCINE (OGAb)
7c: N-OXALYLGLYCINE (OGAc)
7d: N-OXALYLGLYCINE (OGAd)
8a: ZINC ION (ZNa)
8b: ZINC ION (ZNb)
8c: ZINC ION (ZNc)
8d: ZINC ION (ZNd)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
48V
2
Mod. Amino Acid
{[(2R)-2,3-DIAMINO-3-OXOPROPYL]SULFANYL}ACETIC ACID
2
CL
5
Ligand/Ion
CHLORIDE ION
3
DTY
2
Mod. Amino Acid
D-TYROSINE
4
GOL
5
Ligand/Ion
GLYCEROL
5
M3L
4
Mod. Amino Acid
N-TRIMETHYLLYSINE
6
NI
4
Ligand/Ion
NICKEL (II) ION
7
OGA
4
Ligand/Ion
N-OXALYLGLYCINE
8
ZN
4
Ligand/Ion
ZINC ION
[
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Sites
(32, 32)
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)
16: AD7 (SOFTWARE)
17: AD8 (SOFTWARE)
18: AD9 (SOFTWARE)
19: AE1 (SOFTWARE)
20: AE2 (SOFTWARE)
21: AE3 (SOFTWARE)
22: AE4 (SOFTWARE)
23: AE5 (SOFTWARE)
24: AE6 (SOFTWARE)
25: AE7 (SOFTWARE)
26: AE8 (SOFTWARE)
27: AE9 (SOFTWARE)
28: AF1 (SOFTWARE)
29: AF2 (SOFTWARE)
30: AF3 (SOFTWARE)
31: AF4 (SOFTWARE)
32: AF5 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
HIS A:188 , GLU A:190 , HIS A:276 , OGA A:503 , HOH A:663
binding site for residue NI A 501
02
AC2
SOFTWARE
CYS A:234 , HIS A:240 , CYS A:306 , CYS A:308
binding site for residue ZN A 502
03
AC3
SOFTWARE
TYR A:132 , PHE A:185 , HIS A:188 , GLU A:190 , SER A:196 , ASN A:198 , LYS A:206 , HIS A:276 , SER A:288 , NI A:501 , HOH A:663 , M3L E:6 , HOH E:102
binding site for residue OGA A 503
04
AC4
SOFTWARE
ASP A:311 , TYR E:3
binding site for residue GOL A 504
05
AC5
SOFTWARE
TYR A:59 , ASP A:60
binding site for residue GOL A 505
06
AC6
SOFTWARE
GLY A:229 , LYS B:105
binding site for residue CL B 401
07
AC7
SOFTWARE
HIS B:188 , GLU B:190 , HIS B:276 , OGA B:405 , HOH B:545
binding site for residue NI B 402
08
AC8
SOFTWARE
CYS B:234 , HIS B:240 , CYS B:306 , CYS B:308
binding site for residue ZN B 403
09
AC9
SOFTWARE
GLY B:229 , SER B:230
binding site for residue CL B 404
10
AD1
SOFTWARE
TYR B:132 , PHE B:185 , HIS B:188 , GLU B:190 , SER B:196 , ASN B:198 , LYS B:206 , HIS B:276 , NI B:402 , HOH B:545 , M3L F:6
binding site for residue OGA B 405
11
AD2
SOFTWARE
GLY B:138 , THR B:139
binding site for residue GOL B 406
12
AD3
SOFTWARE
ASP B:191 , ARG B:239 , HIS B:240 , CYS B:306 , VAL B:313 , HOH B:527 , ASN F:4 , TRP F:9
binding site for residue GOL B 407
13
AD4
SOFTWARE
TYR B:85 , ASN B:86 , MET B:242 , TRP F:9
binding site for residue GOL B 408
14
AD5
SOFTWARE
HIS C:188 , GLU C:190 , HIS C:276 , OGA C:504 , HOH C:641
binding site for residue NI C 501
15
AD6
SOFTWARE
CYS C:234 , HIS C:240 , CYS C:306 , CYS C:308
binding site for residue ZN C 502
16
AD7
SOFTWARE
TYR C:59 , ARG C:98
binding site for residue CL C 503
17
AD8
SOFTWARE
TYR C:132 , PHE C:185 , HIS C:188 , GLU C:190 , SER C:196 , ASN C:198 , LYS C:206 , TRP C:208 , HIS C:276 , SER C:288 , NI C:501 , HOH C:641 , HOH G:101
binding site for residue OGA C 504
18
AD9
SOFTWARE
PHE C:227 , LYS D:105
binding site for residue CL D 401
19
AE1
SOFTWARE
HIS D:188 , GLU D:190 , HIS D:276 , OGA D:405 , HOH D:528
binding site for residue NI D 402
20
AE2
SOFTWARE
CYS D:234 , HIS D:240 , CYS D:306 , CYS D:308
binding site for residue ZN D 403
21
AE3
SOFTWARE
PHE D:227 , GLY D:229 , SER D:230
binding site for residue CL D 404
22
AE4
SOFTWARE
TYR D:132 , PHE D:185 , HIS D:188 , GLU D:190 , SER D:196 , ASN D:198 , LYS D:206 , SER D:288 , NI D:402 , HOH D:528 , HOH D:561
binding site for residue OGA D 405
23
AE5
SOFTWARE
ASP A:135 , GLY A:170 , TYR A:177 , GLU A:190 , LYS A:241 , SER A:288 , THR A:289 , ASN A:290 , OGA A:503 , THR E:5 , GLY E:8 , HOH E:101 , HOH E:102 , HOH E:103
binding site for Ligand residues M3L E 6 through SER E 7 bound to THR E 5
24
AE6
SOFTWARE
ASN B:86 , ALA B:134 , ASP B:135 , GLY B:170 , TYR B:177 , GLU B:190 , LYS B:241 , SER B:288 , THR B:289 , ASN B:290 , OGA B:405 , HOH B:545 , THR F:5 , GLY F:8 , HOH F:101 , HOH F:102
binding site for Ligand residues M3L F 6 through SER F 7 bound to THR F 5
25
AE7
SOFTWARE
ASP C:135 , TYR C:177 , LYS C:241 , SER C:288 , ASN C:290 , THR G:5 , GLY G:8 , HOH G:101
binding site for Ligand residues M3L G 6 through SER G 7 bound to THR G 5
26
AE8
SOFTWARE
ASP D:135 , GLY D:170 , TYR D:175 , TYR D:177 , GLU D:190 , LYS D:241 , SER D:288 , ASN D:290 , THR H:5 , GLY H:8 , HOH H:101
binding site for Ligand residues M3L H 6 through SER H 7 bound to THR H 5
27
AE9
SOFTWARE
GLN B:88 , DTY E:1 , TYR E:12 , TYR F:3 , ARG F:10
binding site for Di-peptide 48V E 0 and THR E 13
28
AF1
SOFTWARE
GLN B:88 , LYS B:89 , LYS B:90 , HOH B:504 , VAL E:2 , TRP E:11 , TYR E:12 , THR E:13 , TYR F:3
binding site for Di-peptide 48V E 0 and DTY E 1
29
AF2
SOFTWARE
ARG A:309 , GLN B:88 , LYS B:89 , LYS B:90 , HOH B:504 , 48V E:0 , TYR E:3 , ARG E:10 , TRP E:11 , TYR E:12
binding site for Di-peptide DTY E 1 and VAL E 2
30
AF3
SOFTWARE
GLN D:88 , LYS D:90 , HOH D:527 , VAL G:2 , TRP G:11 , TYR G:12 , THR G:13 , TYR H:3
binding site for Di-peptide 48V G 0 and DTY G 1
31
AF4
SOFTWARE
GLN D:88 , DTY G:1 , TYR G:12 , TYR H:3 , ARG H:10
binding site for Di-peptide 48V G 0 and THR G 13
32
AF5
SOFTWARE
ARG C:309 , LYS D:90 , HOH D:527 , 48V G:0 , TYR G:3 , ARG G:10 , TRP G:11 , TYR G:12
binding site for Di-peptide DTY G 1 and VAL G 2
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SAPs(SNPs)/Variants
(0, 0)
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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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