eF-site ID 2y5b-ABEF
PDB Code 2y5b
Chain A, B, E, F

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Title Structure of USP21 in complex with linear diubiquitin-aldehyde
Classification PROTEIN BINDING/HYDROLASE
Compound UBIQUITIN CARBOXYL-TERMINAL HYDROLASE 21
Source Homo sapiens (Human) (UBB_HUMAN)
Sequence A:  HTLLLGSGHVGLRNLGNTCFLNAVLQCLSSTRPLRDFCLR
RDFRQEVRAQELTEAFADVIGALWHPDSCEAVNPTRFRAV
FQKYVPSFSGYSQQDAQEFLKLLMERLHLEINRRSDDDRA
NLMWKRYLEREDSKIVDLFVGQLKSCLKCQACGYRSTTFE
VFCDLSLPIPKKKVSLRDCFNLFTKEEELESENAPVCDRC
RQKTRSTKKLTVQRFPRILVLHLNRFSASRGSIKKSSVGV
DFPLQRLSLGDFASDSPVYQLYALCNHSGSVHYGHYTALC
RCQTGWHVYNDSRVSPVSENQVASSEGYVLFYQLM
B:  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQ
QRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLHMQIFVK
TLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFA
GKQLEDGRTLSDYNIQKESTLHLVLRLRGX
E:  HHTLLLGSGHVGLRNLGNTCFLNAVLQCLSSTRPLRDFCL
RRDFRQERAQELTEAFADVIGALWHPDSCEAVNPTRFRAV
FQKYVPSFSGYSQQDAQEFLKLLMERLHLEINRRGEEPEL
SDDDRANLMWKRYLEREDSKIVDLFVGQLKSCLKCQACGY
RSTTFEVFCDLSLPIPKGKVSLRDCFNLFTKEEELESENA
PVCDRCRQKTRSTKKLTVQRFPRILVLHLNRFSASRGSIK
KSSVGVDFPLQRLSLGDFASDKAGSPVYQLYALCNHSGSV
HYGHYTALCRCQTGWHVYNDSRVSPVSENQVASSEGYVLF
YQLMQ
F:  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQ
QRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGHMQIF
VKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLI
FAGKQLEDGRTLSDYNIQKESTLHLVLRLRGX
Description


Functional site

1) chain A
residue 384
type
sequence C
description BINDING SITE FOR RESIDUE ZN A 1000
source : AC1

2) chain A
residue 387
type
sequence C
description BINDING SITE FOR RESIDUE ZN A 1000
source : AC1

3) chain A
residue 437
type
sequence C
description BINDING SITE FOR RESIDUE ZN A 1000
source : AC1

4) chain A
residue 440
type
sequence C
description BINDING SITE FOR RESIDUE ZN A 1000
source : AC1

5) chain A
residue 472
type
sequence S
description BINDING SITE FOR RESIDUE SO4 A 1559
source : AC2

6) chain A
residue 473
type
sequence I
description BINDING SITE FOR RESIDUE SO4 A 1559
source : AC2

7) chain A
residue 474
type
sequence K
description BINDING SITE FOR RESIDUE SO4 A 1560
source : AC3

8) chain A
residue 475
type
sequence K
description BINDING SITE FOR RESIDUE SO4 A 1560
source : AC3

9) chain A
residue 513
type
sequence S
description BINDING SITE FOR RESIDUE SO4 A 1560
source : AC3

10) chain A
residue 514
type
sequence V
description BINDING SITE FOR RESIDUE SO4 A 1560
source : AC3

11) chain F
residue 54
type
sequence R
description BINDING SITE FOR RESIDUE SO4 A 1560
source : AC3

12) chain E
residue 235
type
sequence P
description BINDING SITE FOR RESIDUE SO4 E 1560
source : AC4

13) chain E
residue 369
type
sequence K
description BINDING SITE FOR RESIDUE SO4 E 1560
source : AC4

14) chain E
residue 457
type
sequence R
description BINDING SITE FOR RESIDUE SO4 E 1560
source : AC4

15) chain E
residue 276
type
sequence E
description BINDING SITE FOR RESIDUE SO4 E 1561
source : AC5

16) chain E
residue 277
type
sequence A
description BINDING SITE FOR RESIDUE SO4 E 1561
source : AC5

17) chain A
residue 320
type
sequence R
description BINDING SITE FOR RESIDUE SO4 A 1561
source : AC6

18) chain A
residue 235
type
sequence P
description BINDING SITE FOR RESIDUE SO4 A 1562
source : AC7

19) chain A
residue 369
type
sequence K
description BINDING SITE FOR RESIDUE SO4 A 1562
source : AC7

20) chain A
residue 457
type
sequence R
description BINDING SITE FOR RESIDUE SO4 A 1562
source : AC7

21) chain A
residue 483
type
sequence P
description BINDING SITE FOR RESIDUE SO4 A 1563
source : AC8

22) chain A
residue 484
type
sequence L
description BINDING SITE FOR RESIDUE SO4 A 1563
source : AC8

23) chain A
residue 485
type
sequence Q
description BINDING SITE FOR RESIDUE SO4 A 1563
source : AC8

24) chain E
residue 320
type
sequence R
description BINDING SITE FOR RESIDUE SO4 E 1562
source : AC9

25) chain A
residue 541
type
sequence S
description BINDING SITE FOR RESIDUE SO4 A 1564
source : BC1

26) chain A
residue 543
type
sequence N
description BINDING SITE FOR RESIDUE SO4 A 1564
source : BC1

27) chain E
residue 296
type
sequence G
description BINDING SITE FOR RESIDUE SO4 A 1564
source : BC1

28) chain A
residue 515
type
sequence H
description BINDING SITE FOR RESIDUE SO4 B 1152
source : BC2

29) chain B
residue 116
type
sequence Q
description BINDING SITE FOR RESIDUE SO4 B 1152
source : BC2

30) chain B
residue 150
type
sequence R
description BINDING SITE FOR RESIDUE SO4 B 1152
source : BC2

31) chain F
residue 116
type
sequence Q
description BINDING SITE FOR RESIDUE SO4 F 1152
source : BC3

32) chain F
residue 148
type
sequence R
description BINDING SITE FOR RESIDUE SO4 F 1152
source : BC3

33) chain F
residue 150
type
sequence R
description BINDING SITE FOR RESIDUE SO4 F 1152
source : BC3

34) chain A
residue 215
type
sequence R
description BINDING SITE FOR RESIDUE SO4 A 1565
source : BC4

35) chain A
residue 216
type
sequence N
description BINDING SITE FOR RESIDUE SO4 A 1565
source : BC4

36) chain A
residue 390
type
sequence R
description BINDING SITE FOR RESIDUE SO4 A 1565
source : BC4

37) chain A
residue 534
type
sequence D
description BINDING SITE FOR RESIDUE SO4 A 1565
source : BC4

38) chain A
residue 535
type
sequence S
description BINDING SITE FOR RESIDUE SO4 A 1565
source : BC4

39) chain E
residue 384
type
sequence C
description BINDING SITE FOR RESIDUE ZN E 1000
source : BC5

40) chain E
residue 387
type
sequence C
description BINDING SITE FOR RESIDUE ZN E 1000
source : BC5

41) chain E
residue 437
type
sequence C
description BINDING SITE FOR RESIDUE ZN E 1000
source : BC5

42) chain E
residue 440
type
sequence C
description BINDING SITE FOR RESIDUE ZN E 1000
source : BC5

43) chain B
residue 27-52
type prosite
sequence KAKIQDKEGIPPDQQRLIFAGKQLED
description UBIQUITIN_1 Ubiquitin domain signature. KakIqDkegIPpdqQrLIFaGkqleD
source prosite : PS00299

44) chain B
residue 103-128
type prosite
sequence KAKIQDKEGIPPDQQRLIFAGKQLED
description UBIQUITIN_1 Ubiquitin domain signature. KakIqDkegIPpdqQrLIFaGkqleD
source prosite : PS00299

45) chain A
residue 213-228
type prosite
sequence GLRNLGNTCFLNAVLQ
description USP_1 Ubiquitin specific protease (USP) domain signature 1. GLrnlGNtCFLNAvLQ
source prosite : PS00972

46) chain A
residue 502-519
type prosite
sequence YQLYALCNHSGSVHYGHY
description USP_2 Ubiquitin specific protease (USP) domain signature 2. YqLyALcnHsGsvhy..GHY
source prosite : PS00973

47) chain B
residue 54
type SITE
sequence R
description Interacts with activating enzyme
source Swiss-Prot : SWS_FT_FI1

48) chain B
residue 72
type SITE
sequence R
description Interacts with activating enzyme
source Swiss-Prot : SWS_FT_FI1

49) chain F
residue 54
type SITE
sequence R
description Interacts with activating enzyme
source Swiss-Prot : SWS_FT_FI1

50) chain F
residue 72
type SITE
sequence R
description Interacts with activating enzyme
source Swiss-Prot : SWS_FT_FI1

51) chain B
residue 29
type CROSSLNK
sequence K
description Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) => ECO:0000269|PubMed:16543144, ECO:0000269|PubMed:25752573, ECO:0000269|PubMed:25752577, ECO:0000269|PubMed:34239127
source Swiss-Prot : SWS_FT_FI10

52) chain F
residue 29
type CROSSLNK
sequence K
description Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) => ECO:0000269|PubMed:16543144, ECO:0000269|PubMed:25752573, ECO:0000269|PubMed:25752577, ECO:0000269|PubMed:34239127
source Swiss-Prot : SWS_FT_FI10

53) chain B
residue 33
type CROSSLNK
sequence K
description Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) => ECO:0000269|PubMed:25752577
source Swiss-Prot : SWS_FT_FI11

54) chain F
residue 33
type CROSSLNK
sequence K
description Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) => ECO:0000269|PubMed:25752577
source Swiss-Prot : SWS_FT_FI11

55) chain B
residue 63
type CROSSLNK
sequence K
description Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) => ECO:0000269|PubMed:16543144, ECO:0000269|PubMed:18719106
source Swiss-Prot : SWS_FT_FI12

56) chain F
residue 63
type CROSSLNK
sequence K
description Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) => ECO:0000269|PubMed:16543144, ECO:0000269|PubMed:18719106
source Swiss-Prot : SWS_FT_FI12

57) chain B
residue 68
type SITE
sequence H
description Essential for function
source Swiss-Prot : SWS_FT_FI2

58) chain F
residue 68
type SITE
sequence H
description Essential for function
source Swiss-Prot : SWS_FT_FI2

59) chain B
residue 65
type MOD_RES
sequence S
description Phosphoserine; by PINK1 => ECO:0000269|PubMed:24660806, ECO:0000269|PubMed:24751536, ECO:0000269|PubMed:24784582, ECO:0000269|PubMed:25527291
source Swiss-Prot : SWS_FT_FI3

60) chain F
residue 65
type MOD_RES
sequence S
description Phosphoserine; by PINK1 => ECO:0000269|PubMed:24660806, ECO:0000269|PubMed:24751536, ECO:0000269|PubMed:24784582, ECO:0000269|PubMed:25527291
source Swiss-Prot : SWS_FT_FI3

61) chain A
residue 437
type MOD_RES
sequence C
description Phosphoserine; by PINK1 => ECO:0000269|PubMed:24660806, ECO:0000269|PubMed:24751536, ECO:0000269|PubMed:24784582, ECO:0000269|PubMed:25527291
source Swiss-Prot : SWS_FT_FI3

62) chain A
residue 440
type MOD_RES
sequence C
description Phosphoserine; by PINK1 => ECO:0000269|PubMed:24660806, ECO:0000269|PubMed:24751536, ECO:0000269|PubMed:24784582, ECO:0000269|PubMed:25527291
source Swiss-Prot : SWS_FT_FI3

63) chain E
residue 384
type MOD_RES
sequence C
description Phosphoserine; by PINK1 => ECO:0000269|PubMed:24660806, ECO:0000269|PubMed:24751536, ECO:0000269|PubMed:24784582, ECO:0000269|PubMed:25527291
source Swiss-Prot : SWS_FT_FI3

64) chain E
residue 387
type MOD_RES
sequence C
description Phosphoserine; by PINK1 => ECO:0000269|PubMed:24660806, ECO:0000269|PubMed:24751536, ECO:0000269|PubMed:24784582, ECO:0000269|PubMed:25527291
source Swiss-Prot : SWS_FT_FI3

65) chain E
residue 437
type MOD_RES
sequence C
description Phosphoserine; by PINK1 => ECO:0000269|PubMed:24660806, ECO:0000269|PubMed:24751536, ECO:0000269|PubMed:24784582, ECO:0000269|PubMed:25527291
source Swiss-Prot : SWS_FT_FI3

66) chain E
residue 440
type MOD_RES
sequence C
description Phosphoserine; by PINK1 => ECO:0000269|PubMed:24660806, ECO:0000269|PubMed:24751536, ECO:0000269|PubMed:24784582, ECO:0000269|PubMed:25527291
source Swiss-Prot : SWS_FT_FI3

67) chain B
residue 66
type MOD_RES
sequence T
description (Microbial infection) ADP-ribosylthreonine => ECO:0000269|PubMed:32330457
source Swiss-Prot : SWS_FT_FI4

68) chain F
residue 66
type MOD_RES
sequence T
description (Microbial infection) ADP-ribosylthreonine => ECO:0000269|PubMed:32330457
source Swiss-Prot : SWS_FT_FI4

69) chain B
residue 76
type MOD_RES
sequence H
description ADP-ribosylglycine => ECO:0000269|PubMed:28525742
source Swiss-Prot : SWS_FT_FI5

70) chain F
residue 76
type MOD_RES
sequence H
description ADP-ribosylglycine => ECO:0000269|PubMed:28525742
source Swiss-Prot : SWS_FT_FI5

71) chain B
residue 6
type CROSSLNK
sequence K
description Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) => ECO:0000269|PubMed:16443603
source Swiss-Prot : SWS_FT_FI6

72) chain F
residue 6
type CROSSLNK
sequence K
description Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) => ECO:0000269|PubMed:16443603
source Swiss-Prot : SWS_FT_FI6

73) chain B
residue 76
type CROSSLNK
sequence H
description Glycyl lysine isopeptide (Gly-Lys) (interchain with K-? in acceptor proteins)
source Swiss-Prot : SWS_FT_FI7

74) chain F
residue 76
type CROSSLNK
sequence H
description Glycyl lysine isopeptide (Gly-Lys) (interchain with K-? in acceptor proteins)
source Swiss-Prot : SWS_FT_FI7

75) chain B
residue 11
type CROSSLNK
sequence K
description Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) => ECO:0000269|PubMed:16443603, ECO:0000269|PubMed:16543144
source Swiss-Prot : SWS_FT_FI8

76) chain B
residue 48
type CROSSLNK
sequence K
description Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) => ECO:0000269|PubMed:16443603, ECO:0000269|PubMed:16543144
source Swiss-Prot : SWS_FT_FI8

77) chain F
residue 11
type CROSSLNK
sequence K
description Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) => ECO:0000269|PubMed:16443603, ECO:0000269|PubMed:16543144
source Swiss-Prot : SWS_FT_FI8

78) chain F
residue 48
type CROSSLNK
sequence K
description Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) => ECO:0000269|PubMed:16443603, ECO:0000269|PubMed:16543144
source Swiss-Prot : SWS_FT_FI8

79) chain B
residue 27
type CROSSLNK
sequence K
description Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) => ECO:0000305|PubMed:15466860
source Swiss-Prot : SWS_FT_FI9

80) chain F
residue 27
type CROSSLNK
sequence K
description Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) => ECO:0000305|PubMed:15466860
source Swiss-Prot : SWS_FT_FI9


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