eF-site ID 6idv-AB
PDB Code 6idv
Chain A, B

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Title Peptide Asparaginyl Ligases from Viola yedoensis
Classification LIGASE
Compound Peptide Asparaginyl Ligases
Source (6IDV)
Sequence A:  IGTRWAVLIAGSKGYHNYRHQADVCHMYQILRKGGVKDEN
IIVFMYDDIAYNESNPFPGIIINKPGGENVYKGVPKDYTG
EDINNVNFLAAILGNKSAIIGGSGKVLDTSPNDHIFIYYA
HGAPGKIGMPSKPYLYADDLVDTLKQKAATGTYKSMVFYV
EACNAGSMFEGLLPEGTNIYAMAASNSTEGSWITYCPGTP
DFPPEFDVCLGDLWSITFLEDCDAHNLRTETVHQQFELVK
KKIAYASTVSQYGDIPISKDSLSVYMGTDPANDNRTFVPL
KVIHQHDADLYHIWCKYNMAPEGSSKKIEAQKQLLELMSH
RAHVDNSITLIGKLLFGVNKASKVLNTVRPVGQPLVDDWQ
CLKAMIRTFETHCGSLSEYGMKHTLSFANMCNAGIQKEQL
AEAAAQACVTFPSNPYSSLAEGFSA
B:  GTRWAVLIAGSKGYHNYRHQADVCHMYQILRKGGVKDENI
IVFMYDDIAYNESNPFPGIIINKPGGENVYKGVPKDYTGE
DINNVNFLAAILGNKSAIIGGSGKVLDTSPNDHIFIYYAH
GAPGKIGMPSKPYLYADDLVDTLKQKAATGTYKSMVFYVE
ACNAGSMFEGLLPEGTNIYAMAASNSTEGSWITYCPGTPD
FPPEFDVCLGDLWSITFLEDCDAHNLRTETVHQQFELVKK
KIAYASTVSQYGDIPISKDSLSVYMGTDPANDNRTFVDPL
KVIHQHDADLYHIWCKYNMAPEGSSKKIEAQKQLLELMSH
RAHVDNSITLIGKLLFGVNKASKVLNTVRPVGQPLVDDWQ
CLKAMIRTFETHCGSLSEYGMKHTLSFANMCNAGIQKEQL
AEAAAQACVTFPSNPYSSLAEGFSA
Description (1)  Peptide Asparaginyl Ligases


Functional site

1) chain A
residue 145
type
ligand
sequence N
description binding site for residue NAG A 504
source : AC1

2) chain A
residue 61
type
ligand
sequence G
description binding site for residue SNN A 505
source : AC2

3) chain A
residue 70
type
ligand
sequence H
description binding site for residue SNN A 505
source : AC2

4) chain A
residue 169
type
ligand
sequence Y
description binding site for residue SNN A 505
source : AC2

5) chain A
residue 170
type
ligand
sequence A
description binding site for residue SNN A 505
source : AC2

6) chain A
residue 172
type
ligand
sequence H
description binding site for residue SNN A 505
source : AC2

7) chain A
residue 173
type
ligand
sequence G
description binding site for residue SNN A 505
source : AC2

8) chain A
residue 179
type
ligand
sequence G
description binding site for residue SNN A 505
source : AC2

9) chain A
residue 212
type
ligand
sequence E
description binding site for residue SNN A 505
source : AC2

10) chain A
residue 213
type
ligand
sequence A
description binding site for residue SNN A 505
source : AC2

11) chain A
residue 343
type
ligand
sequence Q
description binding site for residue SNN A 505
source : AC2

12) chain A
residue 415
type
ligand
sequence D
description binding site for residue EDO A 506
source : AC3

13) chain A
residue 416
type
ligand
sequence D
description binding site for residue EDO A 506
source : AC3

14) chain A
residue 417
type
ligand
sequence W
description binding site for residue EDO A 506
source : AC3

15) chain B
residue 145
type
ligand
sequence N
description binding site for residue NAG B 702
source : AC4

16) chain A
residue 129
type
ligand
sequence T
description binding site for residue PEG B 704
source : AC5

17) chain A
residue 131
type
ligand
sequence E
description binding site for residue PEG B 704
source : AC5

18) chain A
residue 132
type
ligand
sequence D
description binding site for residue PEG B 704
source : AC5

19) chain B
residue 129
type
ligand
sequence T
description binding site for residue PEG B 704
source : AC5

20) chain B
residue 132
type
ligand
sequence D
description binding site for residue PEG B 704
source : AC5

21) chain A
residue 65
type
ligand
sequence Y
description binding site for Poly-Saccharide residues NAG A 507 through NAG A 508 bound to ASN A 102
source : AC6

22) chain A
residue 98
type
ligand
sequence D
description binding site for Poly-Saccharide residues NAG A 507 through NAG A 508 bound to ASN A 102
source : AC6

23) chain A
residue 101
type
ligand
sequence Y
description binding site for Poly-Saccharide residues NAG A 507 through NAG A 508 bound to ASN A 102
source : AC6

24) chain A
residue 102
type
ligand
sequence N
description binding site for Poly-Saccharide residues NAG A 507 through NAG A 508 bound to ASN A 102
source : AC6

25) chain A
residue 103
type
ligand
sequence E
description binding site for Poly-Saccharide residues NAG A 507 through NAG A 508 bound to ASN A 102
source : AC6

26) chain B
residue 153
type
ligand
sequence S
description binding site for Poly-Saccharide residues NAG A 507 through NAG A 508 bound to ASN A 102
source : AC6

27) chain A
residue 237
type
ligand
sequence N
description binding site for Poly-Saccharide residues NAG A 501 through FUC A 503 bound to ASN A 237
source : AC7

28) chain A
residue 239
type
ligand
sequence T
description binding site for Poly-Saccharide residues NAG A 501 through FUC A 503 bound to ASN A 237
source : AC7

29) chain A
residue 240
type
ligand
sequence E
description binding site for Poly-Saccharide residues NAG A 501 through FUC A 503 bound to ASN A 237
source : AC7

30) chain A
residue 153
type
ligand
sequence S
description binding site for Poly-Saccharide residues NAG B 706 through FUC B 708 bound to ASN B 102
source : AC8

31) chain B
residue 64
type
ligand
sequence G
description binding site for Poly-Saccharide residues NAG B 706 through FUC B 708 bound to ASN B 102
source : AC8

32) chain B
residue 65
type
ligand
sequence Y
description binding site for Poly-Saccharide residues NAG B 706 through FUC B 708 bound to ASN B 102
source : AC8

33) chain B
residue 101
type
ligand
sequence Y
description binding site for Poly-Saccharide residues NAG B 706 through FUC B 708 bound to ASN B 102
source : AC8

34) chain B
residue 102
type
ligand
sequence N
description binding site for Poly-Saccharide residues NAG B 706 through FUC B 708 bound to ASN B 102
source : AC8

35) chain B
residue 103
type
ligand
sequence E
description binding site for Poly-Saccharide residues NAG B 706 through FUC B 708 bound to ASN B 102
source : AC8

36) chain B
residue 237
type
ligand
sequence N
description binding site for Mono-Saccharide NAG B 701 bound to ASN B 237
source : AC9

37) chain B
residue 238
type
ligand
sequence S
description binding site for Mono-Saccharide NAG B 701 bound to ASN B 237
source : AC9

38) chain B
residue 239
type
ligand
sequence T
description binding site for Mono-Saccharide NAG B 701 bound to ASN B 237
source : AC9

39) chain B
residue 240
type
ligand
sequence E
description binding site for Mono-Saccharide NAG B 701 bound to ASN B 237
source : AC9

40) chain B
residue 61
type
ligand
sequence G
description binding site for Di-peptide SNN B 703 and HIS B 172
source : AD1

41) chain B
residue 67
type
ligand
sequence N
description binding site for Di-peptide SNN B 703 and HIS B 172
source : AD1

42) chain B
residue 70
type
ligand
sequence H
description binding site for Di-peptide SNN B 703 and HIS B 172
source : AD1

43) chain B
residue 169
type
ligand
sequence Y
description binding site for Di-peptide SNN B 703 and HIS B 172
source : AD1

44) chain B
residue 170
type
ligand
sequence A
description binding site for Di-peptide SNN B 703 and HIS B 172
source : AD1

45) chain B
residue 173
type
ligand
sequence G
description binding site for Di-peptide SNN B 703 and HIS B 172
source : AD1

46) chain B
residue 178
type
ligand
sequence I
description binding site for Di-peptide SNN B 703 and HIS B 172
source : AD1

47) chain B
residue 179
type
ligand
sequence G
description binding site for Di-peptide SNN B 703 and HIS B 172
source : AD1

48) chain B
residue 212
type
ligand
sequence E
description binding site for Di-peptide SNN B 703 and HIS B 172
source : AD1

49) chain B
residue 213
type
ligand
sequence A
description binding site for Di-peptide SNN B 703 and HIS B 172
source : AD1

50) chain B
residue 343
type
ligand
sequence Q
description binding site for Di-peptide SNN B 703 and HIS B 172
source : AD1

51) chain B
residue 436
type
ligand
sequence E
description binding site for Di-peptide SNN B 703 and HIS B 172
source : AD1

52) chain B
residue 59
type
ligand
sequence I
description binding site for Di-peptide SNN B 703 and ALA B 170
source : AD2

53) chain B
residue 60
type
ligand
sequence A
description binding site for Di-peptide SNN B 703 and ALA B 170
source : AD2

54) chain B
residue 61
type
ligand
sequence G
description binding site for Di-peptide SNN B 703 and ALA B 170
source : AD2

55) chain B
residue 70
type
ligand
sequence H
description binding site for Di-peptide SNN B 703 and ALA B 170
source : AD2

56) chain B
residue 168
type
ligand
sequence Y
description binding site for Di-peptide SNN B 703 and ALA B 170
source : AD2

57) chain B
residue 169
type
ligand
sequence Y
description binding site for Di-peptide SNN B 703 and ALA B 170
source : AD2

58) chain B
residue 172
type
ligand
sequence H
description binding site for Di-peptide SNN B 703 and ALA B 170
source : AD2

59) chain B
residue 173
type
ligand
sequence G
description binding site for Di-peptide SNN B 703 and ALA B 170
source : AD2

60) chain B
residue 179
type
ligand
sequence G
description binding site for Di-peptide SNN B 703 and ALA B 170
source : AD2

61) chain B
residue 212
type
ligand
sequence E
description binding site for Di-peptide SNN B 703 and ALA B 170
source : AD2

62) chain B
residue 213
type
ligand
sequence A
description binding site for Di-peptide SNN B 703 and ALA B 170
source : AD2

63) chain B
residue 343
type
ligand
sequence Q
description binding site for Di-peptide SNN B 703 and ALA B 170
source : AD2

64) chain A
residue 60-62
type binding
ligand SNN: L-3-AMINOSUCCINIMIDE
sequence AGS
description L-3-AMINOSUCCINIMIDE binding site
source pdb_hetatom : SNN_6idv_A_505

65) chain A
residue 70
type binding
ligand SNN: L-3-AMINOSUCCINIMIDE
sequence H
description L-3-AMINOSUCCINIMIDE binding site
source pdb_hetatom : SNN_6idv_A_505

66) chain A
residue 169-170
type binding
ligand SNN: L-3-AMINOSUCCINIMIDE
sequence YA
description L-3-AMINOSUCCINIMIDE binding site
source pdb_hetatom : SNN_6idv_A_505

67) chain A
residue 172-173
type binding
ligand SNN: L-3-AMINOSUCCINIMIDE
sequence HG
description L-3-AMINOSUCCINIMIDE binding site
source pdb_hetatom : SNN_6idv_A_505

68) chain A
residue 177
type binding
ligand SNN: L-3-AMINOSUCCINIMIDE
sequence K
description L-3-AMINOSUCCINIMIDE binding site
source pdb_hetatom : SNN_6idv_A_505

69) chain A
residue 179-180
type binding
ligand SNN: L-3-AMINOSUCCINIMIDE
sequence GM
description L-3-AMINOSUCCINIMIDE binding site
source pdb_hetatom : SNN_6idv_A_505

70) chain A
residue 212-214
type binding
ligand SNN: L-3-AMINOSUCCINIMIDE
sequence EAC
description L-3-AMINOSUCCINIMIDE binding site
source pdb_hetatom : SNN_6idv_A_505

71) chain A
residue 343
type binding
ligand SNN: L-3-AMINOSUCCINIMIDE
sequence Q
description L-3-AMINOSUCCINIMIDE binding site
source pdb_hetatom : SNN_6idv_A_505

72) chain A
residue 64-66
type binding
ligand NAG: N-ACETYL-D-GLUCOSAMINE
sequence GYH
description N-ACETYL-D-GLUCOSAMINE binding site
source pdb_hetatom : NAG_6idv_A_507

73) chain A
residue 97-98
type binding
ligand NAG: N-ACETYL-D-GLUCOSAMINE
sequence DD
description N-ACETYL-D-GLUCOSAMINE binding site
source pdb_hetatom : NAG_6idv_A_507

74) chain A
residue 101-103
type binding
ligand NAG: N-ACETYL-D-GLUCOSAMINE
sequence YNE
description N-ACETYL-D-GLUCOSAMINE binding site
source pdb_hetatom : NAG_6idv_A_507

75) chain B
residue 146
type binding
ligand NAG: N-ACETYL-D-GLUCOSAMINE
sequence K
description N-ACETYL-D-GLUCOSAMINE binding site
source pdb_hetatom : NAG_6idv_A_507

76) chain B
residue 152-154
type binding
ligand NAG: N-ACETYL-D-GLUCOSAMINE
sequence GSG
description N-ACETYL-D-GLUCOSAMINE binding site
source pdb_hetatom : NAG_6idv_A_507

77) chain A
residue 96
type binding
ligand PEG: DI(HYDROXYETHYL)ETHER
sequence Y
description DI(HYDROXYETHYL)ETHER binding site
source pdb_hetatom : PEG_6idv_B_704

78) chain A
residue 129-132
type binding
ligand PEG: DI(HYDROXYETHYL)ETHER
sequence TGED
description DI(HYDROXYETHYL)ETHER binding site
source pdb_hetatom : PEG_6idv_B_704

79) chain B
residue 129-132
type binding
ligand PEG: DI(HYDROXYETHYL)ETHER
sequence TGED
description DI(HYDROXYETHYL)ETHER binding site
source pdb_hetatom : PEG_6idv_B_704

80) chain B
residue 151-152
type binding
ligand PEG: DI(HYDROXYETHYL)ETHER
sequence GG
description DI(HYDROXYETHYL)ETHER binding site
source pdb_hetatom : PEG_6idv_B_704

81) chain A
residue 145
type binding
ligand NAG: N-ACETYL-D-GLUCOSAMINE
sequence N
description N-ACETYL-D-GLUCOSAMINE binding site
source pdb_hetatom : NAG_6idv_A_504

82) chain A
residue 147-148
type binding
ligand NAG: N-ACETYL-D-GLUCOSAMINE
sequence SA
description N-ACETYL-D-GLUCOSAMINE binding site
source pdb_hetatom : NAG_6idv_A_504

83) chain A
residue 152-154
type binding
ligand NAG: N-ACETYL-D-GLUCOSAMINE
sequence GSG
description N-ACETYL-D-GLUCOSAMINE binding site
source pdb_hetatom : NAG_6idv_B_706

84) chain B
residue 64-66
type binding
ligand NAG: N-ACETYL-D-GLUCOSAMINE
sequence GYH
description N-ACETYL-D-GLUCOSAMINE binding site
source pdb_hetatom : NAG_6idv_B_706

85) chain B
residue 98
type binding
ligand NAG: N-ACETYL-D-GLUCOSAMINE
sequence D
description N-ACETYL-D-GLUCOSAMINE binding site
source pdb_hetatom : NAG_6idv_B_706

86) chain B
residue 101-103
type binding
ligand NAG: N-ACETYL-D-GLUCOSAMINE
sequence YNE
description N-ACETYL-D-GLUCOSAMINE binding site
source pdb_hetatom : NAG_6idv_B_706

87) chain A
residue 189
type binding
ligand EDO: 1,2-ETHANEDIOL
sequence D
description 1,2-ETHANEDIOL binding site
source pdb_hetatom : EDO_6idv_A_506

88) chain A
residue 415-418
type binding
ligand EDO: 1,2-ETHANEDIOL
sequence DDWQ
description 1,2-ETHANEDIOL binding site
source pdb_hetatom : EDO_6idv_A_506

89) chain A
residue 237-240
type binding
ligand NAG: N-ACETYL-D-GLUCOSAMINE
sequence NSTE
description N-ACETYL-D-GLUCOSAMINE binding site
source pdb_hetatom : NAG_6idv_A_501

90) chain A
residue 299
type binding
ligand NAG: N-ACETYL-D-GLUCOSAMINE
sequence T
description N-ACETYL-D-GLUCOSAMINE binding site
source pdb_hetatom : NAG_6idv_A_501

91) chain A
residue 406-407
type binding
ligand NAG: N-ACETYL-D-GLUCOSAMINE
sequence VR
description N-ACETYL-D-GLUCOSAMINE binding site
source pdb_hetatom : NAG_6idv_A_501

92) chain A
residue 409
type binding
ligand NAG: N-ACETYL-D-GLUCOSAMINE
sequence V
description N-ACETYL-D-GLUCOSAMINE binding site
source pdb_hetatom : NAG_6idv_A_501

93) chain B
residue 60-62
type binding
ligand SNN: L-3-AMINOSUCCINIMIDE
sequence AGS
description L-3-AMINOSUCCINIMIDE binding site
source pdb_hetatom : SNN_6idv_B_703

94) chain B
residue 70
type binding
ligand SNN: L-3-AMINOSUCCINIMIDE
sequence H
description L-3-AMINOSUCCINIMIDE binding site
source pdb_hetatom : SNN_6idv_B_703

95) chain B
residue 169-170
type binding
ligand SNN: L-3-AMINOSUCCINIMIDE
sequence YA
description L-3-AMINOSUCCINIMIDE binding site
source pdb_hetatom : SNN_6idv_B_703

96) chain B
residue 172-173
type binding
ligand SNN: L-3-AMINOSUCCINIMIDE
sequence HG
description L-3-AMINOSUCCINIMIDE binding site
source pdb_hetatom : SNN_6idv_B_703

97) chain B
residue 179-180
type binding
ligand SNN: L-3-AMINOSUCCINIMIDE
sequence GM
description L-3-AMINOSUCCINIMIDE binding site
source pdb_hetatom : SNN_6idv_B_703

98) chain B
residue 212-214
type binding
ligand SNN: L-3-AMINOSUCCINIMIDE
sequence EAC
description L-3-AMINOSUCCINIMIDE binding site
source pdb_hetatom : SNN_6idv_B_703

99) chain B
residue 242
type binding
ligand SNN: L-3-AMINOSUCCINIMIDE
sequence S
description L-3-AMINOSUCCINIMIDE binding site
source pdb_hetatom : SNN_6idv_B_703

100) chain B
residue 263
type binding
ligand SNN: L-3-AMINOSUCCINIMIDE
sequence D
description L-3-AMINOSUCCINIMIDE binding site
source pdb_hetatom : SNN_6idv_B_703

101) chain B
residue 343
type binding
ligand SNN: L-3-AMINOSUCCINIMIDE
sequence Q
description L-3-AMINOSUCCINIMIDE binding site
source pdb_hetatom : SNN_6idv_B_703

102) chain B
residue 436
type binding
ligand SNN: L-3-AMINOSUCCINIMIDE
sequence E
description L-3-AMINOSUCCINIMIDE binding site
source pdb_hetatom : SNN_6idv_B_703

103) chain B
residue 145
type binding
ligand NAG: N-ACETYL-D-GLUCOSAMINE
sequence N
description N-ACETYL-D-GLUCOSAMINE binding site
source pdb_hetatom : NAG_6idv_B_702

104) chain B
residue 147-148
type binding
ligand NAG: N-ACETYL-D-GLUCOSAMINE
sequence SA
description N-ACETYL-D-GLUCOSAMINE binding site
source pdb_hetatom : NAG_6idv_B_702

105) chain B
residue 221
type binding
ligand NAG: N-ACETYL-D-GLUCOSAMINE
sequence E
description N-ACETYL-D-GLUCOSAMINE binding site
source pdb_hetatom : NAG_6idv_B_701

106) chain B
residue 237-240
type binding
ligand NAG: N-ACETYL-D-GLUCOSAMINE
sequence NSTE
description N-ACETYL-D-GLUCOSAMINE binding site
source pdb_hetatom : NAG_6idv_B_701

107) chain B
residue 299
type binding
ligand NAG: N-ACETYL-D-GLUCOSAMINE
sequence T
description N-ACETYL-D-GLUCOSAMINE binding site
source pdb_hetatom : NAG_6idv_B_701

108) chain B
residue 407
type binding
ligand NAG: N-ACETYL-D-GLUCOSAMINE
sequence R
description N-ACETYL-D-GLUCOSAMINE binding site
source pdb_hetatom : NAG_6idv_B_701

109) chain B
residue 409
type binding
ligand NAG: N-ACETYL-D-GLUCOSAMINE
sequence V
description N-ACETYL-D-GLUCOSAMINE binding site
source pdb_hetatom : NAG_6idv_B_701

110) chain B
residue 284
type binding
ligand EDO: 1,2-ETHANEDIOL
sequence H
description 1,2-ETHANEDIOL binding site
source pdb_hetatom : EDO_6idv_B_705

111) chain B
residue 306-307
type binding
ligand EDO: 1,2-ETHANEDIOL
sequence IP
description 1,2-ETHANEDIOL binding site
source pdb_hetatom : EDO_6idv_B_705

112) chain B
residue 309-310
type binding
ligand EDO: 1,2-ETHANEDIOL
sequence SK
description 1,2-ETHANEDIOL binding site
source pdb_hetatom : EDO_6idv_B_705


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