eF-site ID 3azm-ABCDEFGHIJ
PDB Code 3azm
Chain A, B, C, D, E, F, G, H, I, J

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Title Crystal Structure of Human Nucleosome Core Particle Containing H4K79Q mutation
Classification STRUCTURAL PROTEIN/DNA
Compound Histone H3.1
Source Homo sapiens (Human) (3AZM)
Sequence A:  PHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQD
FKTDLRFQSSAVMALQEACEAYLVGLFEDTNLCAIHAKRV
TIMPKDIQLARRIRGERA
B:  NIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKVFLEN
VIRDAVTYTEHAKRQTVTAMDVVYALKRQGRTLYGFG
C:  KAKTRSSRAGLQFPVGRVHRLLRKGNYSERVGAGAPVYLA
AVLEYLTAEILELAGNAARDNKKTRIIPRHLQLAIRNDEE
LNKLLGRVTIAQGGVLPNIQAVLLPK
D:  KRSRKESYSIYVYKVLKQVHPDTGISSKAMGIMNSFVNDI
FERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKH
AVSEGTKAVTKYTSA
E:  KPHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQ
DFKTDLRFQSSAVMALQEACEAYLVGLFEDTNLCAIHAKR
VTIMPKDIQLARRIRGERA
F:  RKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVL
KVFLENVIRDAVTYTEHAKRQTVTAMDVVYALKRQGRTLY
GFGG
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 121
type
sequence P
description BINDING SITE FOR RESIDUE CL A 1001
source : AC1

2) chain A
residue 122
type
sequence K
description BINDING SITE FOR RESIDUE CL A 1001
source : AC1

3) chain C
residue 44
type
sequence G
description BINDING SITE FOR RESIDUE CL C 1001
source : AC2

4) chain C
residue 45
type
sequence A
description BINDING SITE FOR RESIDUE CL C 1001
source : AC2

5) chain C
residue 46
type
sequence G
description BINDING SITE FOR RESIDUE CL C 1001
source : AC2

6) chain C
residue 47
type
sequence A
description BINDING SITE FOR RESIDUE CL C 1001
source : AC2

7) chain D
residue 91
type
sequence S
description BINDING SITE FOR RESIDUE CL C 1001
source : AC2

8) chain D
residue 48
type
sequence V
description BINDING SITE FOR RESIDUE MN E 1001
source : AC3

9) chain E
residue 77
type
sequence D
description BINDING SITE FOR RESIDUE MN E 1001
source : AC3

10) chain G
residue 44
type
sequence G
description BINDING SITE FOR RESIDUE CL G 1001
source : AC4

11) chain G
residue 45
type
sequence A
description BINDING SITE FOR RESIDUE CL G 1001
source : AC4

12) chain G
residue 46
type
sequence G
description BINDING SITE FOR RESIDUE CL G 1001
source : AC4

13) chain G
residue 47
type
sequence A
description BINDING SITE FOR RESIDUE CL G 1001
source : AC4

14) chain I
residue 100
type
sequence G
description BINDING SITE FOR RESIDUE MN I 1001
source : AC5

15) chain I
residue 121
type
sequence G
description BINDING SITE FOR RESIDUE MN I 1002
source : AC6

16) chain I
residue 133
type
sequence A
description BINDING SITE FOR RESIDUE MN I 1003
source : AC7

17) chain J
residue 267
type
sequence G
description BINDING SITE FOR RESIDUE MN J 1001
source : AC8

18) chain J
residue 279
type
sequence A
description BINDING SITE FOR RESIDUE MN J 1002
source : AC9

19) chain J
residue 280
type
sequence G
description BINDING SITE FOR RESIDUE MN J 1002
source : AC9

20) chain J
residue 217
type
sequence G
description BINDING SITE FOR RESIDUE MN J 1003
source : BC1

21) chain J
residue 218
type
sequence A
description BINDING SITE FOR RESIDUE MN J 1003
source : BC1

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

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

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

25) chain F
residue 20
type CARBOHYD
sequence K
description O-linked (GlcNAc) serine => ECO:0000250|UniProtKB:P62807
source Swiss-Prot : SWS_FT_FI16

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

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

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

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

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

31) 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

32) 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

33) chain A
residue 79
type MOD_RES
sequence K
description N6-succinyllysine; alternate => ECO:0000269|PubMed:22389435, ECO:0000269|PubMed:29211711
source Swiss-Prot : SWS_FT_FI21

34) chain E
residue 79
type MOD_RES
sequence K
description N6-succinyllysine; alternate => ECO:0000269|PubMed:22389435, ECO:0000269|PubMed:29211711
source Swiss-Prot : SWS_FT_FI21

35) chain A
residue 80
type MOD_RES
sequence T
description Phosphothreonine => ECO:0000269|PubMed:20850016
source Swiss-Prot : SWS_FT_FI22

36) chain E
residue 80
type MOD_RES
sequence T
description Phosphothreonine => ECO:0000269|PubMed:20850016
source Swiss-Prot : SWS_FT_FI22

37) chain A
residue 86
type MOD_RES
sequence S
description Phosphoserine => ECO:0000250|UniProtKB:P84243
source Swiss-Prot : SWS_FT_FI23

38) chain E
residue 86
type MOD_RES
sequence S
description Phosphoserine => ECO:0000250|UniProtKB:P84243
source Swiss-Prot : SWS_FT_FI23

39) chain A
residue 107
type MOD_RES
sequence T
description Phosphothreonine => ECO:0000250|UniProtKB:Q71DI3
source Swiss-Prot : SWS_FT_FI24

40) chain E
residue 107
type MOD_RES
sequence T
description Phosphothreonine => ECO:0000250|UniProtKB:Q71DI3
source Swiss-Prot : SWS_FT_FI24

41) chain A
residue 115
type MOD_RES
sequence K
description N6-glutaryllysine; alternate => ECO:0000269|PubMed:31542297
source Swiss-Prot : SWS_FT_FI25

42) chain E
residue 115
type MOD_RES
sequence K
description N6-glutaryllysine; alternate => ECO:0000269|PubMed:31542297
source Swiss-Prot : SWS_FT_FI25

43) chain A
residue 122
type MOD_RES
sequence K
description N6-succinyllysine; alternate => ECO:0000269|PubMed:22389435, ECO:0000269|PubMed:27436229
source Swiss-Prot : SWS_FT_FI26

44) chain E
residue 122
type MOD_RES
sequence K
description N6-succinyllysine; alternate => ECO:0000269|PubMed:22389435, ECO:0000269|PubMed:27436229
source Swiss-Prot : SWS_FT_FI26

45) 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

46) 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

47) chain G
residue 95
type MOD_RES
sequence K
description ADP-ribosylserine => ECO:0000269|PubMed:34874266
source Swiss-Prot : SWS_FT_FI4

48) chain B
residue 44
type MOD_RES
sequence K
description N6-crotonyllysine; alternate => ECO:0000269|PubMed:21925322
source Swiss-Prot : SWS_FT_FI5

49) chain F
residue 44
type MOD_RES
sequence K
description N6-crotonyllysine; alternate => ECO:0000269|PubMed:21925322
source Swiss-Prot : SWS_FT_FI5

50) chain B
residue 77
type MOD_RES
sequence K
description Phosphoserine; by STK4/MST1 => ECO:0000269|PubMed:12757711
source Swiss-Prot : SWS_FT_FI6

51) chain B
residue 91
type MOD_RES
sequence K
description Phosphoserine; by STK4/MST1 => ECO:0000269|PubMed:12757711
source Swiss-Prot : SWS_FT_FI6

52) chain F
residue 31
type MOD_RES
sequence K
description Phosphoserine; by STK4/MST1 => ECO:0000269|PubMed:12757711
source Swiss-Prot : SWS_FT_FI6

53) chain F
residue 77
type MOD_RES
sequence K
description Phosphoserine; by STK4/MST1 => ECO:0000269|PubMed:12757711
source Swiss-Prot : SWS_FT_FI6

54) chain F
residue 91
type MOD_RES
sequence K
description Phosphoserine; by STK4/MST1 => ECO:0000269|PubMed:12757711
source Swiss-Prot : SWS_FT_FI6

55) chain G
residue 74
type MOD_RES
sequence K
description N6-(2-hydroxyisobutyryl)lysine => ECO:0000269|PubMed:24681537
source Swiss-Prot : SWS_FT_FI7

56) chain G
residue 75
type MOD_RES
sequence K
description N6-(2-hydroxyisobutyryl)lysine => ECO:0000269|PubMed:24681537
source Swiss-Prot : SWS_FT_FI7

57) chain D
residue 34
type MOD_RES
sequence K
description N6-succinyllysine; alternate => ECO:0000269|PubMed:22389435
source Swiss-Prot : SWS_FT_FI8

58) chain D
residue 116
type MOD_RES
sequence K
description N6-succinyllysine; alternate => ECO:0000269|PubMed:22389435
source Swiss-Prot : SWS_FT_FI8

59) chain D
residue 120
type MOD_RES
sequence K
description N6-succinyllysine; alternate => ECO:0000269|PubMed:22389435
source Swiss-Prot : SWS_FT_FI8

60) chain H
residue 34
type MOD_RES
sequence K
description N6-succinyllysine; alternate => ECO:0000269|PubMed:22389435
source Swiss-Prot : SWS_FT_FI8

61) chain H
residue 116
type MOD_RES
sequence K
description N6-succinyllysine; alternate => ECO:0000269|PubMed:22389435
source Swiss-Prot : SWS_FT_FI8

62) chain H
residue 120
type MOD_RES
sequence K
description N6-succinyllysine; alternate => ECO:0000269|PubMed:22389435
source Swiss-Prot : SWS_FT_FI8

63) chain D
residue 35
type MOD_RES
sequence E
description PolyADP-ribosyl glutamic acid => ECO:0000250|UniProtKB:Q64475
source Swiss-Prot : SWS_FT_FI9

64) chain H
residue 35
type MOD_RES
sequence E
description PolyADP-ribosyl glutamic acid => ECO:0000250|UniProtKB:Q64475
source Swiss-Prot : SWS_FT_FI9

65) chain G
residue 118
type MOD_RES
sequence K
description PolyADP-ribosyl glutamic acid => ECO:0000250|UniProtKB:Q64475
source Swiss-Prot : SWS_FT_FI9

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

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

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

69) chain D
residue 36
type MOD_RES
sequence S
description Phosphoserine; by AMPK => ECO:0000250|UniProtKB:Q64475
source Swiss-Prot : SWS_FT_FI10

70) chain H
residue 36
type MOD_RES
sequence S
description Phosphoserine; by AMPK => ECO:0000250|UniProtKB:Q64475
source Swiss-Prot : SWS_FT_FI10

71) chain E
residue 56
type MOD_RES
sequence K
description Phosphoserine; by AMPK => ECO:0000250|UniProtKB:Q64475
source Swiss-Prot : SWS_FT_FI10

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

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

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

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

76) 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

77) 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

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

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

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

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

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

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

84) chain H
residue 43
type MOD_RES
sequence K
description N6-lactoyllysine; alternate => ECO:0000269|PubMed:31645732
source Swiss-Prot : SWS_FT_FI3

85) chain H
residue 85
type MOD_RES
sequence K
description N6-lactoyllysine; alternate => ECO:0000269|PubMed:31645732
source Swiss-Prot : SWS_FT_FI3

86) chain D
residue 43
type MOD_RES
sequence K
description N6-lactoyllysine; alternate => ECO:0000269|PubMed:31645732
source Swiss-Prot : SWS_FT_FI3

87) chain D
residue 85
type MOD_RES
sequence K
description N6-lactoyllysine; alternate => ECO:0000269|PubMed:31645732
source Swiss-Prot : SWS_FT_FI3


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