eF-site ID 6g59-A
PDB Code 6g59
Chain A

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

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

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

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

43) 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

44) 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

45) 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

46) 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

47) 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

48) 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

49) 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

50) 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

51) 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

52) 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

53) 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

54) 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

55) 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


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