eF-site ID 6g59-AB
PDB Code 6g59
Chain A, B

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Title Structure of the alanine racemase from Staphylococcus aureus in complex with an pyridoxal-6- phosphate derivative
Classification BIOSYNTHETIC PROTEIN
Compound Alanine racemase 1
Source (ALR1_STAAM)
Sequence A:  YKKAGFSDKYYRSAYMNVDLNAVASNFKVFSTLHPNKTVM
AVVKANAYGLGSVKVARHLMENGATFFAVATLDEAIELRM
HGITAKILVLGVLPAKDIDKAIQHRVALTVPSKQWLKEAI
KNISGEQEKKLWLHIKLDTGMGRLGIKDTNTYQEVIEIIQ
QYEQLVFEGVFTHFACADEPGDMTTEQYQRFKDMVNEAIK
PEYIHCQNSAGSLLMDCQFCNAIRPGISLYGYYPSEYVQQ
KVKVHLKPSVQLIANVVQTKTLQAGESVSYGATYTATDPT
TIALLPIGYADGYLRIMQGSFVNVNGHQCEVIGRVCMDQT
IVKVPDQVKAGDSVILIDNHRESPQSVEVVAEKQHTINYE
VLCNLSRRLPRIYHDGDQRFVTNELLK
B:  AGFSDKYYRSAYMNVDLNAVASNFKVFSTLHPNKTVMAVV
KANAYGLGSVKVARHLMENGATFFAVATLDEAIELRMHGI
TAKILVLGVLPAKDIDKAIQHRVALTVPSKQWLKEAIKNI
SGEQEKKLWLHIKLDTGMGRLGIKDTNTYQEVIEIIQQYE
QLVFEGVFTHFACADEPGDMTTEQYQRFKDMVNEAIKPEY
IHCQNSAGSLLMDCQFCNAIRPGISLYGYYPSEYVQQKVK
VHLKPSVQLIANVVQTKTLQAGESVSYGATYTATDPTTIA
LLPIGYADGYLRIMQGSFVNVNGHQCEVIGRVCMDQTIVK
VPDQVKAGDSVILIDNHRESPQSVEVVAEKQHTINYEVLC
NLSRRLPRIYHDGDQRFVTNELLK
Description (1)  Alanine racemase 1 (E.C.5.1.1.1)


Functional site

1) chain A
residue 39
type
ligand
sequence K
description binding site for residue EM2 A 401
source : AC1

2) chain A
residue 43
type
ligand
sequence Y
description binding site for residue EM2 A 401
source : AC1

3) chain A
residue 168
type
ligand
sequence H
description binding site for residue EM2 A 401
source : AC1

4) chain A
residue 203
type
ligand
sequence N
description binding site for residue EM2 A 401
source : AC1

5) chain A
residue 204
type
ligand
sequence S
description binding site for residue EM2 A 401
source : AC1

6) chain A
residue 219
type
ligand
sequence R
description binding site for residue EM2 A 401
source : AC1

7) chain A
residue 221
type
ligand
sequence G
description binding site for residue EM2 A 401
source : AC1

8) chain A
residue 222
type
ligand
sequence I
description binding site for residue EM2 A 401
source : AC1

9) chain A
residue 354
type
ligand
sequence Y
description binding site for residue EM2 A 401
source : AC1

10) chain A
residue -1
type
ligand
sequence A
description binding site for residue SO4 A 402
source : AC2

11) chain A
residue 0
type
ligand
sequence G
description binding site for residue SO4 A 402
source : AC2

12) chain A
residue 1
type
ligand
sequence F
description binding site for residue SO4 A 402
source : AC2

13) chain A
residue 2
type
ligand
sequence S
description binding site for residue SO4 A 402
source : AC2

14) chain A
residue 4
type
ligand
sequence K
description binding site for residue SO4 A 402
source : AC2

15) chain A
residue 143
type
ligand
sequence D
description binding site for residue SO4 A 402
source : AC2

16) chain A
residue 144
type
ligand
sequence T
description binding site for residue SO4 A 402
source : AC2

17) chain A
residue 185
type
ligand
sequence R
description binding site for residue SO4 A 402
source : AC2

18) chain A
residue 49
type
ligand
sequence K
description binding site for residue SO4 A 403
source : AC3

19) chain A
residue 52
type
ligand
sequence R
description binding site for residue SO4 A 403
source : AC3

20) chain A
residue 76
type
ligand
sequence H
description binding site for residue SO4 A 403
source : AC3

21) chain A
residue 240
type
ligand
sequence H
description binding site for residue SO4 A 404
source : AC4

22) chain A
residue 243
type
ligand
sequence P
description binding site for residue SO4 A 404
source : AC4

23) chain A
residue 335
type
ligand
sequence H
description binding site for residue SO4 A 404
source : AC4

24) chain A
residue 336
type
ligand
sequence R
description binding site for residue SO4 A 404
source : AC4

25) chain A
residue 290
type
ligand
sequence R
description binding site for residue SO4 A 405
source : AC5

26) chain A
residue 291
type
ligand
sequence I
description binding site for residue SO4 A 405
source : AC5

27) chain A
residue 293
type
ligand
sequence Q
description binding site for residue SO4 A 405
source : AC5

28) chain A
residue 309
type
ligand
sequence R
description binding site for residue SO4 A 405
source : AC5

29) chain A
residue 154
type
ligand
sequence I
description binding site for residue NA A 406
source : AC6

30) chain A
residue 157
type
ligand
sequence Y
description binding site for residue NA A 406
source : AC6

31) chain A
residue 160
type
ligand
sequence L
description binding site for residue NA A 406
source : AC6

32) chain A
residue 227
type
ligand
sequence Y
description binding site for residue NA A 407
source : AC7

33) chain A
residue 245
type
ligand
sequence V
description binding site for residue NA A 407
source : AC7

34) chain A
residue 333
type
ligand
sequence D
description binding site for residue NA A 407
source : AC7

35) chain A
residue 334
type
ligand
sequence N
description binding site for residue NA A 407
source : AC7

36) chain A
residue 342
type
ligand
sequence V
description binding site for residue NA A 407
source : AC7

37) chain A
residue 262
type
ligand
sequence S
description binding site for residue NA A 408
source : AC8

38) chain A
residue 264
type
ligand
sequence S
description binding site for residue NA A 408
source : AC8

39) chain B
residue 135
type
ligand
sequence G
description binding site for residue NA A 408
source : AC8

40) chain B
residue 136
type
ligand
sequence M
description binding site for residue NA A 408
source : AC8

41) chain B
residue 170
type
ligand
sequence A
description binding site for residue NA A 408
source : AC8

42) chain A
residue 29
type
ligand
sequence H
description binding site for residue CL A 409
source : AC9

43) chain A
residue 30
type
ligand
sequence P
description binding site for residue CL A 409
source : AC9

44) chain A
residue 31
type
ligand
sequence N
description binding site for residue CL A 409
source : AC9

45) chain B
residue 240
type
ligand
sequence H
description binding site for residue SO4 B 402
source : AD1

46) chain B
residue 243
type
ligand
sequence P
description binding site for residue SO4 B 402
source : AD1

47) chain B
residue 335
type
ligand
sequence H
description binding site for residue SO4 B 402
source : AD1

48) chain B
residue 336
type
ligand
sequence R
description binding site for residue SO4 B 402
source : AD1

49) chain B
residue 5
type
ligand
sequence Y
description binding site for residue SO4 B 403
source : AD2

50) chain B
residue 10
type
ligand
sequence Y
description binding site for residue SO4 B 403
source : AD2

51) chain B
residue 367
type
ligand
sequence I
description binding site for residue SO4 B 403
source : AD2

52) chain B
residue 374
type
ligand
sequence R
description binding site for residue SO4 B 403
source : AD2

53) chain B
residue 154
type
ligand
sequence I
description binding site for residue NA B 404
source : AD3

54) chain B
residue 157
type
ligand
sequence Y
description binding site for residue NA B 404
source : AD3

55) chain B
residue 160
type
ligand
sequence L
description binding site for residue NA B 404
source : AD3

56) chain B
residue 29
type
ligand
sequence H
description binding site for residue CL B 405
source : AD4

57) chain B
residue 31
type
ligand
sequence N
description binding site for residue CL B 405
source : AD4

58) chain B
residue 32
type
ligand
sequence K
description binding site for residue CL B 405
source : AD4

59) chain A
residue 313
type
ligand
sequence D
description binding site for Di-peptide EM2 B 401 and LYS B 39
source : AD5

60) chain B
residue 37
type
ligand
sequence V
description binding site for Di-peptide EM2 B 401 and LYS B 39
source : AD5

61) chain B
residue 38
type
ligand
sequence V
description binding site for Di-peptide EM2 B 401 and LYS B 39
source : AD5

62) chain B
residue 40
type
ligand
sequence A
description binding site for Di-peptide EM2 B 401 and LYS B 39
source : AD5

63) chain B
residue 41
type
ligand
sequence N
description binding site for Di-peptide EM2 B 401 and LYS B 39
source : AD5

64) chain B
residue 42
type
ligand
sequence A
description binding site for Di-peptide EM2 B 401 and LYS B 39
source : AD5

65) chain B
residue 43
type
ligand
sequence Y
description binding site for Di-peptide EM2 B 401 and LYS B 39
source : AD5

66) chain B
residue 63
type
ligand
sequence A
description binding site for Di-peptide EM2 B 401 and LYS B 39
source : AD5

67) chain B
residue 65
type
ligand
sequence A
description binding site for Di-peptide EM2 B 401 and LYS B 39
source : AD5

68) chain B
residue 69
type
ligand
sequence E
description binding site for Di-peptide EM2 B 401 and LYS B 39
source : AD5

69) chain B
residue 168
type
ligand
sequence H
description binding site for Di-peptide EM2 B 401 and LYS B 39
source : AD5

70) chain B
residue 203
type
ligand
sequence N
description binding site for Di-peptide EM2 B 401 and LYS B 39
source : AD5

71) chain B
residue 204
type
ligand
sequence S
description binding site for Di-peptide EM2 B 401 and LYS B 39
source : AD5

72) chain B
residue 219
type
ligand
sequence R
description binding site for Di-peptide EM2 B 401 and LYS B 39
source : AD5

73) chain B
residue 221
type
ligand
sequence G
description binding site for Di-peptide EM2 B 401 and LYS B 39
source : AD5

74) chain B
residue 222
type
ligand
sequence I
description binding site for Di-peptide EM2 B 401 and LYS B 39
source : AD5

75) chain B
residue 354
type
ligand
sequence Y
description binding site for Di-peptide EM2 B 401 and LYS B 39
source : AD5

76) chain A
residue 37
type binding
ligand EM2: (6-ethynyl-4-methanoyl-5-oxidanyl-pyridin-3-yl)methyl dihydrogen phosphate
sequence V
description (6-ethynyl-4-methanoyl-5-oxidanyl-pyridin-3-yl)methyl dihydrogen phosphate binding site
source pdb_hetatom : EM2_6g59_A_401

77) chain A
residue 39
type binding
ligand EM2: (6-ethynyl-4-methanoyl-5-oxidanyl-pyridin-3-yl)methyl dihydrogen phosphate
sequence K
description (6-ethynyl-4-methanoyl-5-oxidanyl-pyridin-3-yl)methyl dihydrogen phosphate binding site
source pdb_hetatom : EM2_6g59_A_401

78) chain A
residue 43
type binding
ligand EM2: (6-ethynyl-4-methanoyl-5-oxidanyl-pyridin-3-yl)methyl dihydrogen phosphate
sequence Y
description (6-ethynyl-4-methanoyl-5-oxidanyl-pyridin-3-yl)methyl dihydrogen phosphate binding site
source pdb_hetatom : EM2_6g59_A_401

79) chain A
residue 85
type binding
ligand EM2: (6-ethynyl-4-methanoyl-5-oxidanyl-pyridin-3-yl)methyl dihydrogen phosphate
sequence L
description (6-ethynyl-4-methanoyl-5-oxidanyl-pyridin-3-yl)methyl dihydrogen phosphate binding site
source pdb_hetatom : EM2_6g59_A_401

80) chain A
residue 131
type binding
ligand EM2: (6-ethynyl-4-methanoyl-5-oxidanyl-pyridin-3-yl)methyl dihydrogen phosphate
sequence K
description (6-ethynyl-4-methanoyl-5-oxidanyl-pyridin-3-yl)methyl dihydrogen phosphate binding site
source pdb_hetatom : EM2_6g59_A_401

81) chain A
residue 166
type binding
ligand EM2: (6-ethynyl-4-methanoyl-5-oxidanyl-pyridin-3-yl)methyl dihydrogen phosphate
sequence F
description (6-ethynyl-4-methanoyl-5-oxidanyl-pyridin-3-yl)methyl dihydrogen phosphate binding site
source pdb_hetatom : EM2_6g59_A_401

82) chain A
residue 168
type binding
ligand EM2: (6-ethynyl-4-methanoyl-5-oxidanyl-pyridin-3-yl)methyl dihydrogen phosphate
sequence H
description (6-ethynyl-4-methanoyl-5-oxidanyl-pyridin-3-yl)methyl dihydrogen phosphate binding site
source pdb_hetatom : EM2_6g59_A_401

83) chain A
residue 203-205
type binding
ligand EM2: (6-ethynyl-4-methanoyl-5-oxidanyl-pyridin-3-yl)methyl dihydrogen phosphate
sequence NSA
description (6-ethynyl-4-methanoyl-5-oxidanyl-pyridin-3-yl)methyl dihydrogen phosphate binding site
source pdb_hetatom : EM2_6g59_A_401

84) chain A
residue 219-223
type binding
ligand EM2: (6-ethynyl-4-methanoyl-5-oxidanyl-pyridin-3-yl)methyl dihydrogen phosphate
sequence RPGIS
description (6-ethynyl-4-methanoyl-5-oxidanyl-pyridin-3-yl)methyl dihydrogen phosphate binding site
source pdb_hetatom : EM2_6g59_A_401

85) chain A
residue 229
type binding
ligand EM2: (6-ethynyl-4-methanoyl-5-oxidanyl-pyridin-3-yl)methyl dihydrogen phosphate
sequence P
description (6-ethynyl-4-methanoyl-5-oxidanyl-pyridin-3-yl)methyl dihydrogen phosphate binding site
source pdb_hetatom : EM2_6g59_A_401

86) chain A
residue 354
type binding
ligand EM2: (6-ethynyl-4-methanoyl-5-oxidanyl-pyridin-3-yl)methyl dihydrogen phosphate
sequence Y
description (6-ethynyl-4-methanoyl-5-oxidanyl-pyridin-3-yl)methyl dihydrogen phosphate binding site
source pdb_hetatom : EM2_6g59_A_401

87) chain B
residue 265
type binding
ligand EM2: (6-ethynyl-4-methanoyl-5-oxidanyl-pyridin-3-yl)methyl dihydrogen phosphate
sequence Y
description (6-ethynyl-4-methanoyl-5-oxidanyl-pyridin-3-yl)methyl dihydrogen phosphate binding site
source pdb_hetatom : EM2_6g59_A_401

88) chain B
residue 313
type binding
ligand EM2: (6-ethynyl-4-methanoyl-5-oxidanyl-pyridin-3-yl)methyl dihydrogen phosphate
sequence D
description (6-ethynyl-4-methanoyl-5-oxidanyl-pyridin-3-yl)methyl dihydrogen phosphate binding site
source pdb_hetatom : EM2_6g59_A_401

89) chain A
residue 265
type binding
ligand EM2: (6-ethynyl-4-methanoyl-5-oxidanyl-pyridin-3-yl)methyl dihydrogen phosphate
sequence Y
description (6-ethynyl-4-methanoyl-5-oxidanyl-pyridin-3-yl)methyl dihydrogen phosphate binding site
source pdb_hetatom : EM2_6g59_B_401

90) chain A
residue 313
type binding
ligand EM2: (6-ethynyl-4-methanoyl-5-oxidanyl-pyridin-3-yl)methyl dihydrogen phosphate
sequence D
description (6-ethynyl-4-methanoyl-5-oxidanyl-pyridin-3-yl)methyl dihydrogen phosphate binding site
source pdb_hetatom : EM2_6g59_B_401

91) chain B
residue 37
type binding
ligand EM2: (6-ethynyl-4-methanoyl-5-oxidanyl-pyridin-3-yl)methyl dihydrogen phosphate
sequence V
description (6-ethynyl-4-methanoyl-5-oxidanyl-pyridin-3-yl)methyl dihydrogen phosphate binding site
source pdb_hetatom : EM2_6g59_B_401

92) chain B
residue 39
type binding
ligand EM2: (6-ethynyl-4-methanoyl-5-oxidanyl-pyridin-3-yl)methyl dihydrogen phosphate
sequence K
description (6-ethynyl-4-methanoyl-5-oxidanyl-pyridin-3-yl)methyl dihydrogen phosphate binding site
source pdb_hetatom : EM2_6g59_B_401

93) chain B
residue 43
type binding
ligand EM2: (6-ethynyl-4-methanoyl-5-oxidanyl-pyridin-3-yl)methyl dihydrogen phosphate
sequence Y
description (6-ethynyl-4-methanoyl-5-oxidanyl-pyridin-3-yl)methyl dihydrogen phosphate binding site
source pdb_hetatom : EM2_6g59_B_401

94) chain B
residue 85
type binding
ligand EM2: (6-ethynyl-4-methanoyl-5-oxidanyl-pyridin-3-yl)methyl dihydrogen phosphate
sequence L
description (6-ethynyl-4-methanoyl-5-oxidanyl-pyridin-3-yl)methyl dihydrogen phosphate binding site
source pdb_hetatom : EM2_6g59_B_401

95) chain B
residue 131
type binding
ligand EM2: (6-ethynyl-4-methanoyl-5-oxidanyl-pyridin-3-yl)methyl dihydrogen phosphate
sequence K
description (6-ethynyl-4-methanoyl-5-oxidanyl-pyridin-3-yl)methyl dihydrogen phosphate binding site
source pdb_hetatom : EM2_6g59_B_401

96) chain B
residue 138
type binding
ligand EM2: (6-ethynyl-4-methanoyl-5-oxidanyl-pyridin-3-yl)methyl dihydrogen phosphate
sequence R
description (6-ethynyl-4-methanoyl-5-oxidanyl-pyridin-3-yl)methyl dihydrogen phosphate binding site
source pdb_hetatom : EM2_6g59_B_401

97) chain B
residue 166
type binding
ligand EM2: (6-ethynyl-4-methanoyl-5-oxidanyl-pyridin-3-yl)methyl dihydrogen phosphate
sequence F
description (6-ethynyl-4-methanoyl-5-oxidanyl-pyridin-3-yl)methyl dihydrogen phosphate binding site
source pdb_hetatom : EM2_6g59_B_401

98) chain B
residue 168
type binding
ligand EM2: (6-ethynyl-4-methanoyl-5-oxidanyl-pyridin-3-yl)methyl dihydrogen phosphate
sequence H
description (6-ethynyl-4-methanoyl-5-oxidanyl-pyridin-3-yl)methyl dihydrogen phosphate binding site
source pdb_hetatom : EM2_6g59_B_401

99) chain B
residue 203-205
type binding
ligand EM2: (6-ethynyl-4-methanoyl-5-oxidanyl-pyridin-3-yl)methyl dihydrogen phosphate
sequence NSA
description (6-ethynyl-4-methanoyl-5-oxidanyl-pyridin-3-yl)methyl dihydrogen phosphate binding site
source pdb_hetatom : EM2_6g59_B_401

100) chain B
residue 219-222
type binding
ligand EM2: (6-ethynyl-4-methanoyl-5-oxidanyl-pyridin-3-yl)methyl dihydrogen phosphate
sequence RPGI
description (6-ethynyl-4-methanoyl-5-oxidanyl-pyridin-3-yl)methyl dihydrogen phosphate binding site
source pdb_hetatom : EM2_6g59_B_401

101) chain B
residue 229
type binding
ligand EM2: (6-ethynyl-4-methanoyl-5-oxidanyl-pyridin-3-yl)methyl dihydrogen phosphate
sequence P
description (6-ethynyl-4-methanoyl-5-oxidanyl-pyridin-3-yl)methyl dihydrogen phosphate binding site
source pdb_hetatom : EM2_6g59_B_401

102) chain B
residue 354
type binding
ligand EM2: (6-ethynyl-4-methanoyl-5-oxidanyl-pyridin-3-yl)methyl dihydrogen phosphate
sequence Y
description (6-ethynyl-4-methanoyl-5-oxidanyl-pyridin-3-yl)methyl dihydrogen phosphate binding site
source pdb_hetatom : EM2_6g59_B_401


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