eF-site ID 5yko-AP
PDB Code 5yko
Chain A, P

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Title Crystal structure of Arabidopsis thaliana JMJ14 catalytic domain in complex with NOG and H3K4me3 peptide
Classification GENE REGULATION
Compound Probable lysine-specific demethylase JMJ14
Source Arabidopsis thaliana (Mouse-ear cress) (H32_ARATH)
Sequence A:  RWNPSEACRPLVDDAPIFYPTNEDFDDPLGYIEKLRSKAE
SYGICRIVPPVAWRPPCPLKEKKIWENSKFPTRIQFIDLL
QNRFGFQTGPDFTLAAFQKYDEYFKECYFQPKVKDLEGEY
WRIVEQATDEVEVYYGADLETKKFGSGFPKYKPGYPISEA
DQYSQCGWNLNNLSRLPGSVLAFESCDISGVIVPWLYVGM
CFSTFCWHVEDHHLYSMNYLHTGDPKVWYGIPGNHAESFE
NVMKKRLPDLFEEQPDLLHQLVTQLSPRILKEEGVPVYRA
VQRSGEFILTFPKAYHSGFNCGFNCAEAVNVAPVDWLVHG
QNAVEGYSKQRRKSSLSHDKLLLGAAMEATYCLWELSLSK
KKTPVIARWKRVCSEDGLLTKAVKKRVQMEEERLNHLQDG
FSLRKMEGDFDNKRERECFLCFYDLHMSASSCKCSPNRFA
CLIHAKDLCSCESKDRYILIRHTLDELWALVRALEGDLDA
IDLWASK
P:  ARTXQTA
Description


Functional site

1) chain A
residue 309
type
sequence H
description binding site for residue NI A 800
source : AC1

2) chain A
residue 311
type
sequence E
description binding site for residue NI A 800
source : AC1

3) chain A
residue 397
type
sequence H
description binding site for residue NI A 800
source : AC1

4) chain A
residue 519
type
sequence C
description binding site for residue ZN A 801
source : AC2

5) chain A
residue 522
type
sequence C
description binding site for residue ZN A 801
source : AC2

6) chain A
residue 542
type
sequence C
description binding site for residue ZN A 801
source : AC2

7) chain A
residue 545
type
sequence H
description binding site for residue ZN A 801
source : AC2

8) chain A
residue 533
type
sequence C
description binding site for residue ZN A 802
source : AC3

9) chain A
residue 535
type
sequence C
description binding site for residue ZN A 802
source : AC3

10) chain A
residue 550
type
sequence C
description binding site for residue ZN A 802
source : AC3

11) chain A
residue 552
type
sequence C
description binding site for residue ZN A 802
source : AC3

12) chain A
residue 236
type
sequence Y
description binding site for residue OGA A 803
source : AC4

13) chain A
residue 298
type
sequence Y
description binding site for residue OGA A 803
source : AC4

14) chain A
residue 306
type
sequence F
description binding site for residue OGA A 803
source : AC4

15) chain A
residue 309
type
sequence H
description binding site for residue OGA A 803
source : AC4

16) chain A
residue 311
type
sequence E
description binding site for residue OGA A 803
source : AC4

17) chain A
residue 317
type
sequence S
description binding site for residue OGA A 803
source : AC4

18) chain A
residue 319
type
sequence N
description binding site for residue OGA A 803
source : AC4

19) chain A
residue 327
type
sequence K
description binding site for residue OGA A 803
source : AC4

20) chain A
residue 329
type
sequence W
description binding site for residue OGA A 803
source : AC4

21) chain A
residue 397
type
sequence H
description binding site for residue OGA A 803
source : AC4

22) chain A
residue 409
type
sequence A
description binding site for residue OGA A 803
source : AC4

23) chain P
residue 4
type
sequence X
description binding site for residue OGA A 803
source : AC4

24) chain P
residue 4
type MOD_RES
sequence X
description N6-methyllysine; alternate => ECO:0000269|PubMed:12581305, ECO:0000269|PubMed:14712277, ECO:0000269|PubMed:15598823, ECO:0000269|PubMed:16258034
source Swiss-Prot : SWS_FT_FI1

25) chain A
residue 311
type MOD_RES
sequence E
description N6-methyllysine; alternate => ECO:0000269|PubMed:12456661, ECO:0000269|PubMed:12581305, ECO:0000269|PubMed:14712277, ECO:0000269|PubMed:15014946, ECO:0000269|PubMed:15598823
source Swiss-Prot : SWS_FT_FI2

26) chain A
residue 397
type MOD_RES
sequence H
description N6-methyllysine; alternate => ECO:0000269|PubMed:12456661, ECO:0000269|PubMed:12581305, ECO:0000269|PubMed:14712277, ECO:0000269|PubMed:15014946, ECO:0000269|PubMed:15598823
source Swiss-Prot : SWS_FT_FI2

27) chain A
residue 522
type MOD_RES
sequence C
description Phosphoserine => ECO:0000269|PubMed:14610360, ECO:0000269|PubMed:15753571
source Swiss-Prot : SWS_FT_FI3

28) chain A
residue 533
type MOD_RES
sequence C
description Phosphoserine => ECO:0000269|PubMed:14610360, ECO:0000269|PubMed:15753571
source Swiss-Prot : SWS_FT_FI3

29) chain A
residue 535
type MOD_RES
sequence C
description Phosphoserine => ECO:0000269|PubMed:14610360, ECO:0000269|PubMed:15753571
source Swiss-Prot : SWS_FT_FI3

30) chain A
residue 542
type MOD_RES
sequence C
description Phosphoserine => ECO:0000269|PubMed:14610360, ECO:0000269|PubMed:15753571
source Swiss-Prot : SWS_FT_FI3

31) chain A
residue 545
type MOD_RES
sequence H
description Phosphoserine => ECO:0000269|PubMed:14610360, ECO:0000269|PubMed:15753571
source Swiss-Prot : SWS_FT_FI3

32) chain A
residue 550
type BINDING
sequence C
description BINDING => ECO:0000269|PubMed:29233856, ECO:0007744|PDB:5YKO
source Swiss-Prot : SWS_FT_FI4

33) chain A
residue 552
type BINDING
sequence C
description BINDING => ECO:0000269|PubMed:29233856, ECO:0007744|PDB:5YKN
source Swiss-Prot : SWS_FT_FI5

34) chain A
residue 171
type SITE
sequence F
description Involved in histone H3A7 recognition => ECO:0000269|PubMed:29233856, ECO:0007744|PDB:5YKN, ECO:0007744|PDB:5YKO
source Swiss-Prot : SWS_FT_FI6

35) chain A
residue 363
type SITE
sequence V
description Involved in histone H3A7 recognition => ECO:0000269|PubMed:29233856, ECO:0007744|PDB:5YKN, ECO:0007744|PDB:5YKO
source Swiss-Prot : SWS_FT_FI6

36) chain A
residue 285
type SITE
sequence E
description Involved in histone H3R2 recognition => ECO:0000269|PubMed:29233856, ECO:0007744|PDB:5YKN, ECO:0007744|PDB:5YKO
source Swiss-Prot : SWS_FT_FI7

37) chain A
residue 516
type SITE
sequence E
description Involved in histone H3R2 recognition => ECO:0000269|PubMed:29233856, ECO:0007744|PDB:5YKN, ECO:0007744|PDB:5YKO
source Swiss-Prot : SWS_FT_FI7

38) chain A
residue 290
type SITE
sequence S
description Involved in histone H3K4me3 recognition => ECO:0000269|PubMed:29233856, ECO:0007744|PDB:5YKN, ECO:0007744|PDB:5YKO
source Swiss-Prot : SWS_FT_FI8

39) chain A
residue 298
type SITE
sequence Y
description Involved in histone H3K4me3 recognition => ECO:0000269|PubMed:29233856, ECO:0007744|PDB:5YKN, ECO:0007744|PDB:5YKO
source Swiss-Prot : SWS_FT_FI8

40) chain A
residue 312
type SITE
sequence D
description Involved in histone H3Q5 recognition => ECO:0000269|PubMed:29233856, ECO:0007744|PDB:5YKN, ECO:0007744|PDB:5YKO
source Swiss-Prot : SWS_FT_FI9


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