eF-site ID 5ay8-ABCDEFGHIJ
PDB Code 5ay8
Chain A, B, C, D, E, F, G, H, I, J

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Title Crystal structure of human nucleosome containing H3.Y
Classification DNA BINDING PROTEIN/DNA
Compound H3.Y
Source (5AY8)
Sequence A:  PHRYKPGTLALREIRKYQKSTQLLLRKLPFQRLVREIAQA
ISPDLRFQSAAIGALQEASEAYLVQLFEDTNLCAIHARRV
TIMPRDMQLARRLRREG
B:  NIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKVFLEN
VIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG
C:  AKTRSSRAGLQFPVGRVHRLLRKGNYSERVGAGAPVYLAA
VLEYLTAEILELAGNAARDNKKTRIIPRHLQLAIRNDEEL
NKLLGRVTIAQGGVLPNIQAVLLPK
D:  RKESYSIYVYKVLKQVHPDTGISSKAMGIMNSFVNDIFER
IAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVS
EGTKAVTKYTSA
E:  PHRYKPGTLALREIRKYQKSTQLLLRKLPFQRLVREIAQA
ISPDLRFQSAAIGALQEASEAYLVQLFEDTNLCAIHARRV
TIMPRDMQLARRLRRE
F:  DNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKVFLE
NVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG
G:  KTRSSRAGLQFPVGRVHRLLRKGNYSERVGAGAPVYLAAV
LEYLTAEILELAGNAARDNKKTRIIPRHLQLAIRNDEELN
KLLGRVTIAQGGVLPNIQAVLLPK
H:  RKESYSIYVYKVLKQVHPDTGISSKAMGIMNSFVNDIFER
IAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVS
EGTKAVTKYTSA
I:  ATCAATATCCACCTGCAGATTCTACCAAAAGTGTATTTGG
AAACTGCTCCATCAAAAGGCATGTTCAGCTGAATTCAGCT
GAACATGCCTTTTGATGGAGCAGTTTCCAAATACACTTTT
GGTAGAATCTGCAGGTGGATATTGA
J:  TCAATATCCACCTGCAGATTCTACCAAAAGTGTATTTGGA
AACTGCTCCATCAAAAGGCATGTTCAGCTGAATTCAGCTG
AACATGCCTTTTGATGGAGCAGTTTCCAAATACACTTTTG
GTAGAATCTGCAGGTGGATATTGAT
Description


Functional site

1) chain A
residue 63
type
sequence R
description binding site for residue MN A 201
source : AC1

2) chain B
residue 28
type
sequence G
description binding site for residue MN A 201
source : AC1

3) chain B
residue 30
type
sequence T
description binding site for residue MN A 201
source : AC1

4) chain B
residue 33
type
sequence A
description binding site for residue MN A 201
source : AC1

5) chain G
residue 45
type
sequence A
description binding site for residue MN G 201
source : AC2

6) chain G
residue 46
type
sequence G
description binding site for residue MN G 201
source : AC2

7) chain G
residue 47
type
sequence A
description binding site for residue MN G 201
source : AC2

8) chain H
residue 90
type
sequence T
description binding site for residue MN G 201
source : AC2

9) chain H
residue 91
type
sequence S
description binding site for residue MN G 201
source : AC2

10) chain I
residue 15
type
sequence G
description binding site for residue MN I 202
source : AC3

11) chain I
residue 16
type
sequence C
description binding site for residue MN I 202
source : AC3

12) chain J
residue 283
type
sequence G
description binding site for residue MN J 301
source : AC4

13) chain J
residue 283
type
sequence G
description binding site for residue MN J 302
source : AC5

14) chain J
residue 280
type
sequence G
description binding site for residue MN J 303
source : AC6

15) chain J
residue 246
type
sequence G
description binding site for residue MN J 304
source : AC7

16) chain J
residue 290
type
sequence G
description binding site for residue CL J 305
source : AC8

17) chain J
residue 218
type
sequence A
description binding site for residue CL J 306
source : AC9

18) chain D
residue 120
type CROSSLNK
sequence K
description Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin); alternate => ECO:0000269|PubMed:16307923, ECO:0000269|PubMed:16627869, ECO:0000269|PubMed:16713563
source Swiss-Prot : SWS_FT_FI18

19) chain H
residue 120
type CROSSLNK
sequence K
description Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin); alternate => ECO:0000269|PubMed:16307923, ECO:0000269|PubMed:16627869, ECO:0000269|PubMed:16713563
source Swiss-Prot : SWS_FT_FI18

20) chain D
residue 34
type CROSSLNK
sequence K
description Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin); alternate => ECO:0000269|PubMed:21726816
source Swiss-Prot : SWS_FT_FI20

21) chain H
residue 34
type CROSSLNK
sequence K
description Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin); alternate => ECO:0000269|PubMed:21726816
source Swiss-Prot : SWS_FT_FI20

22) chain A
residue 107
type MOD_RES
sequence T
description Phosphothreonine => ECO:0000250|UniProtKB:Q71DI3
source Swiss-Prot : SWS_FT_FI10

23) chain E
residue 107
type MOD_RES
sequence T
description Phosphothreonine => ECO:0000250|UniProtKB:Q71DI3
source Swiss-Prot : SWS_FT_FI10

24) chain E
residue 64
type MOD_RES
sequence K
description N6-methyllysine; alternate => ECO:0000250|UniProtKB:P84243
source Swiss-Prot : SWS_FT_FI3

25) chain H
residue 43
type MOD_RES
sequence K
description N6-methyllysine; alternate => ECO:0000250|UniProtKB:P84243
source Swiss-Prot : SWS_FT_FI3

26) chain H
residue 85
type MOD_RES
sequence K
description N6-methyllysine; alternate => ECO:0000250|UniProtKB:P84243
source Swiss-Prot : SWS_FT_FI3

27) chain A
residue 64
type MOD_RES
sequence K
description N6-methyllysine; alternate => ECO:0000250|UniProtKB:P84243
source Swiss-Prot : SWS_FT_FI3

28) chain G
residue 95
type MOD_RES
sequence K
description 5-glutamyl serotonin; alternate => ECO:0000250|UniProtKB:P68431
source Swiss-Prot : SWS_FT_FI4

29) chain B
residue 44
type MOD_RES
sequence K
description Symmetric dimethylarginine => ECO:0000250|UniProtKB:P84244
source Swiss-Prot : SWS_FT_FI5

30) chain F
residue 44
type MOD_RES
sequence K
description Symmetric dimethylarginine => ECO:0000250|UniProtKB:P84244
source Swiss-Prot : SWS_FT_FI5

31) chain B
residue 77
type MOD_RES
sequence K
description N6-methyllysine => ECO:0000250|UniProtKB:P68431
source Swiss-Prot : SWS_FT_FI6

32) chain B
residue 91
type MOD_RES
sequence K
description N6-methyllysine => ECO:0000250|UniProtKB:P68431
source Swiss-Prot : SWS_FT_FI6

33) chain F
residue 31
type MOD_RES
sequence K
description N6-methyllysine => ECO:0000250|UniProtKB:P68431
source Swiss-Prot : SWS_FT_FI6

34) chain F
residue 77
type MOD_RES
sequence K
description N6-methyllysine => ECO:0000250|UniProtKB:P68431
source Swiss-Prot : SWS_FT_FI6

35) chain F
residue 91
type MOD_RES
sequence K
description N6-methyllysine => ECO:0000250|UniProtKB:P68431
source Swiss-Prot : SWS_FT_FI6

36) chain A
residue 41
type MOD_RES
sequence Y
description Phosphotyrosine => ECO:0000250|UniProtKB:P84243
source Swiss-Prot : SWS_FT_FI7

37) chain E
residue 41
type MOD_RES
sequence Y
description Phosphotyrosine => ECO:0000250|UniProtKB:P84243
source Swiss-Prot : SWS_FT_FI7

38) chain G
residue 74
type MOD_RES
sequence K
description Phosphotyrosine => ECO:0000250|UniProtKB:P84243
source Swiss-Prot : SWS_FT_FI7

39) chain G
residue 75
type MOD_RES
sequence K
description Phosphotyrosine => ECO:0000250|UniProtKB:P84243
source Swiss-Prot : SWS_FT_FI7

40) chain A
residue 56
type MOD_RES
sequence K
description N6-succinyllysine; alternate => ECO:0000250|UniProtKB:P84243
source Swiss-Prot : SWS_FT_FI8

41) chain E
residue 56
type MOD_RES
sequence K
description N6-succinyllysine; alternate => ECO:0000250|UniProtKB:P84243
source Swiss-Prot : SWS_FT_FI8

42) chain D
residue 120
type MOD_RES
sequence K
description N6-succinyllysine; alternate => ECO:0000250|UniProtKB:P84243
source Swiss-Prot : SWS_FT_FI8

43) chain H
residue 34
type MOD_RES
sequence K
description N6-succinyllysine; alternate => ECO:0000250|UniProtKB:P84243
source Swiss-Prot : SWS_FT_FI8

44) chain H
residue 116
type MOD_RES
sequence K
description N6-succinyllysine; alternate => ECO:0000250|UniProtKB:P84243
source Swiss-Prot : SWS_FT_FI8

45) chain H
residue 120
type MOD_RES
sequence K
description N6-succinyllysine; alternate => ECO:0000250|UniProtKB:P84243
source Swiss-Prot : SWS_FT_FI8

46) chain A
residue 57
type MOD_RES
sequence S
description Phosphoserine => ECO:0000250|UniProtKB:P84243
source Swiss-Prot : SWS_FT_FI9

47) chain A
residue 86
type MOD_RES
sequence S
description Phosphoserine => ECO:0000250|UniProtKB:P84243
source Swiss-Prot : SWS_FT_FI9

48) chain E
residue 57
type MOD_RES
sequence S
description Phosphoserine => ECO:0000250|UniProtKB:P84243
source Swiss-Prot : SWS_FT_FI9

49) chain E
residue 86
type MOD_RES
sequence S
description Phosphoserine => ECO:0000250|UniProtKB:P84243
source Swiss-Prot : SWS_FT_FI9

50) chain A
residue 66-74
type prosite
sequence PFQRLVREI
description HISTONE_H3_2 Histone H3 signature 2. PFqRLVREI
source prosite : PS00959

51) chain D
residue 92-114
type prosite
sequence REIQTAVRLLLPGELAKHAVSEG
description HISTONE_H2B Histone H2B signature. REIQTavRlLLpGELaKHAVSEG
source prosite : PS00357

52) chain C
residue 21-27
type prosite
sequence AGLQFPV
description HISTONE_H2A Histone H2A signature. AGLqFPV
source prosite : PS00046

53) chain D
residue 112
type CARBOHYD
sequence S
description O-linked (GlcNAc) serine => ECO:0000250|UniProtKB:P62807
source Swiss-Prot : SWS_FT_FI16

54) chain H
residue 112
type CARBOHYD
sequence S
description O-linked (GlcNAc) serine => ECO:0000250|UniProtKB:P62807
source Swiss-Prot : SWS_FT_FI16

55) chain B
residue 79
type CARBOHYD
sequence K
description O-linked (GlcNAc) serine => ECO:0000250|UniProtKB:P62807
source Swiss-Prot : SWS_FT_FI16

56) chain F
residue 59
type CARBOHYD
sequence K
description O-linked (GlcNAc) serine => ECO:0000250|UniProtKB:P62807
source Swiss-Prot : SWS_FT_FI16

57) chain F
residue 79
type CARBOHYD
sequence K
description O-linked (GlcNAc) serine => ECO:0000250|UniProtKB:P62807
source Swiss-Prot : SWS_FT_FI16

58) chain D
residue 46
type MOD_RES
sequence K
description N6-methyllysine; alternate => ECO:0000269|PubMed:16627869
source Swiss-Prot : SWS_FT_FI11

59) chain D
residue 108
type MOD_RES
sequence K
description N6-methyllysine; alternate => ECO:0000269|PubMed:16627869
source Swiss-Prot : SWS_FT_FI11

60) chain H
residue 46
type MOD_RES
sequence K
description N6-methyllysine; alternate => ECO:0000269|PubMed:16627869
source Swiss-Prot : SWS_FT_FI11

61) chain H
residue 108
type MOD_RES
sequence K
description N6-methyllysine; alternate => ECO:0000269|PubMed:16627869
source Swiss-Prot : SWS_FT_FI11

62) chain D
residue 57
type MOD_RES
sequence K
description N6-(2-hydroxyisobutyryl)lysine; alternate => ECO:0000269|PubMed:24681537
source Swiss-Prot : SWS_FT_FI12

63) chain H
residue 57
type MOD_RES
sequence K
description N6-(2-hydroxyisobutyryl)lysine; alternate => ECO:0000269|PubMed:24681537
source Swiss-Prot : SWS_FT_FI12

64) chain D
residue 79
type MOD_RES
sequence R
description Dimethylated arginine => ECO:0000250|UniProtKB:Q96A08
source Swiss-Prot : SWS_FT_FI13

65) chain H
residue 79
type MOD_RES
sequence R
description Dimethylated arginine => ECO:0000250|UniProtKB:Q96A08
source Swiss-Prot : SWS_FT_FI13

66) chain D
residue 86
type MOD_RES
sequence R
description Omega-N-methylarginine => ECO:0000250|UniProtKB:Q96A08
source Swiss-Prot : SWS_FT_FI14

67) chain D
residue 92
type MOD_RES
sequence R
description Omega-N-methylarginine => ECO:0000250|UniProtKB:Q96A08
source Swiss-Prot : SWS_FT_FI14

68) chain H
residue 86
type MOD_RES
sequence R
description Omega-N-methylarginine => ECO:0000250|UniProtKB:Q96A08
source Swiss-Prot : SWS_FT_FI14

69) chain H
residue 92
type MOD_RES
sequence R
description Omega-N-methylarginine => ECO:0000250|UniProtKB:Q96A08
source Swiss-Prot : SWS_FT_FI14

70) chain D
residue 115
type MOD_RES
sequence T
description Phosphothreonine => ECO:0000250|UniProtKB:Q00729
source Swiss-Prot : SWS_FT_FI15

71) chain H
residue 115
type MOD_RES
sequence T
description Phosphothreonine => ECO:0000250|UniProtKB:Q00729
source Swiss-Prot : SWS_FT_FI15

72) chain F
residue 91
type MOD_RES
sequence K
description Phosphothreonine => ECO:0000250|UniProtKB:Q00729
source Swiss-Prot : SWS_FT_FI15


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