eF-site ID 1ldc-A
PDB Code 1ldc
Chain A

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Title X-RAY STRUCTURE OF TWO COMPLEXES OF THE Y143F FLAVOCYTOCHROME B2 MUTANT CRYSTALLIZED IN THE PRESENCE OF LACTATE OR PHENYL-LACTATE
Classification OXIDOREDUCTASE
Compound L-LACTATE DEHYDROGENASE
Source Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) (CYB2_YEAST)
Sequence A:  KISPAEVAKHNKPDDCWVVINGYVYDLTRFLPNHPGGQDV
IKFNAGKDVTAIFEPLHAPNVIDKYIAPEKKLGPLQGSMP
PELVCPPYAPGETKEDIARKEQLKSLLPPLDNIINLYDFE
YLASQTLTKQAWAFYSSGANDEVTHRENHNAYHRIFFKPK
ILVDVRKVDISTDMLGSHVDVPFYVSATALCKLGNPLEGE
KDVARGCGQGVTKVPQMISTLASCSPEEIIEAAPSDKQIQ
WYQLYVNSDRKITDDLVKNVEKLGVKALFVTVDAPSLGQR
EKDMKLKALSKFIDPSLTWKDIEELKKKTKLPIVIKGVQR
TEDVIKAAEIGVSGVVLSNHGGRQLDFSRAPIEVLAETMP
ILEQRNLKDKLEVFVDGGVRRGTDVLKALCLGAKGVGLGR
PFLYANSCYGRNGVEKAIEILRDEIEMSMRLLGVTSIAEL
KPDLLDLSTLKARTVGVPNDVLYNEVYEGPTLTEFEDA
Description (1)  L-LACTATE DEHYDROGENASE: CYTOCHROME C OXIDOREDUCTASE (FLAVOCYTOCHROME B2) (E.C.1.1.2.3) MUTANT WITH TYR 143 REPLACED BY PHE (Y143F) COMPLEXED WITH PYRUVATE


Functional site

1) chain A
residue 144
type
ligand
sequence Y
description BINDING SITE FOR RESIDUE FMN A 570
source : AC1

2) chain A
residue 195
type
ligand
sequence S
description BINDING SITE FOR RESIDUE FMN A 570
source : AC1

3) chain A
residue 196
type
ligand
sequence A
description BINDING SITE FOR RESIDUE FMN A 570
source : AC1

4) chain A
residue 197
type
ligand
sequence T
description BINDING SITE FOR RESIDUE FMN A 570
source : AC1

5) chain A
residue 198
type
ligand
sequence A
description BINDING SITE FOR RESIDUE FMN A 570
source : AC1

6) chain A
residue 228
type
ligand
sequence S
description BINDING SITE FOR RESIDUE FMN A 570
source : AC1

7) chain A
residue 252
type
ligand
sequence Q
description BINDING SITE FOR RESIDUE FMN A 570
source : AC1

8) chain A
residue 280
type
ligand
sequence T
description BINDING SITE FOR RESIDUE FMN A 570
source : AC1

9) chain A
residue 349
type
ligand
sequence K
description BINDING SITE FOR RESIDUE FMN A 570
source : AC1

10) chain A
residue 371
type
ligand
sequence S
description BINDING SITE FOR RESIDUE FMN A 570
source : AC1

11) chain A
residue 373
type
ligand
sequence H
description BINDING SITE FOR RESIDUE FMN A 570
source : AC1

12) chain A
residue 374
type
ligand
sequence G
description BINDING SITE FOR RESIDUE FMN A 570
source : AC1

13) chain A
residue 376
type
ligand
sequence R
description BINDING SITE FOR RESIDUE FMN A 570
source : AC1

14) chain A
residue 409
type
ligand
sequence D
description BINDING SITE FOR RESIDUE FMN A 570
source : AC1

15) chain A
residue 410
type
ligand
sequence G
description BINDING SITE FOR RESIDUE FMN A 570
source : AC1

16) chain A
residue 411
type
ligand
sequence G
description BINDING SITE FOR RESIDUE FMN A 570
source : AC1

17) chain A
residue 413
type
ligand
sequence R
description BINDING SITE FOR RESIDUE FMN A 570
source : AC1

18) chain A
residue 432
type
ligand
sequence G
description BINDING SITE FOR RESIDUE FMN A 570
source : AC1

19) chain A
residue 433
type
ligand
sequence R
description BINDING SITE FOR RESIDUE FMN A 570
source : AC1

20) chain A
residue 36
type
ligand
sequence L
description BINDING SITE FOR RESIDUE HEM A 560
source : AC2

21) chain A
residue 39
type
ligand
sequence F
description BINDING SITE FOR RESIDUE HEM A 560
source : AC2

22) chain A
residue 43
type
ligand
sequence H
description BINDING SITE FOR RESIDUE HEM A 560
source : AC2

23) chain A
residue 44
type
ligand
sequence P
description BINDING SITE FOR RESIDUE HEM A 560
source : AC2

24) chain A
residue 49
type
ligand
sequence V
description BINDING SITE FOR RESIDUE HEM A 560
source : AC2

25) chain A
residue 62
type
ligand
sequence F
description BINDING SITE FOR RESIDUE HEM A 560
source : AC2

26) chain A
residue 66
type
ligand
sequence H
description BINDING SITE FOR RESIDUE HEM A 560
source : AC2

27) chain A
residue 70
type
ligand
sequence V
description BINDING SITE FOR RESIDUE HEM A 560
source : AC2

28) chain A
residue 71
type
ligand
sequence I
description BINDING SITE FOR RESIDUE HEM A 560
source : AC2

29) chain A
residue 75
type
ligand
sequence I
description BINDING SITE FOR RESIDUE HEM A 560
source : AC2

30) chain A
residue 97
type
ligand
sequence Y
description BINDING SITE FOR RESIDUE HEM A 560
source : AC2

31) chain A
residue 139
type
ligand
sequence Q
description BINDING SITE FOR RESIDUE HEM A 560
source : AC2

32) chain A
residue 199
type
ligand
sequence L
description BINDING SITE FOR RESIDUE HEM A 560
source : AC2

33) chain A
residue 230
type
ligand
sequence L
description BINDING SITE FOR RESIDUE HEM A 560
source : AC2

34) chain A
residue 296
type
ligand
sequence K
description BINDING SITE FOR RESIDUE HEM A 560
source : AC2

35) chain A
residue 143
type
ligand
sequence F
description BINDING SITE FOR RESIDUE PYR A 580
source : AC3

36) chain A
residue 254
type
ligand
sequence Y
description BINDING SITE FOR RESIDUE PYR A 580
source : AC3

37) chain A
residue 289
type
ligand
sequence R
description BINDING SITE FOR RESIDUE PYR A 580
source : AC3

38) chain A
residue 373
type
ligand
sequence H
description BINDING SITE FOR RESIDUE PYR A 580
source : AC3

39) chain A
residue 376
type
ligand
sequence R
description BINDING SITE FOR RESIDUE PYR A 580
source : AC3

40) chain A
residue 373
type ACT_SITE
ligand
sequence H
description Proton acceptor.
source Swiss-Prot : SWS_FT_FI1

41) chain A
residue 43
type METAL
ligand
sequence H
description Iron (heme axial ligand) (By similarity)
source Swiss-Prot : SWS_FT_FI2

42) chain A
residue 66
type METAL
ligand
sequence H
description Iron (heme axial ligand) (By similarity)
source Swiss-Prot : SWS_FT_FI2

43) chain A
residue 376
type BINDING
ligand
sequence R
description Substrate.
source Swiss-Prot : SWS_FT_FI3

44) chain A
residue 371-377
type prosite
ligand
sequence SNHGGRQ
description FMN-dependent alpha-hydroxy acid dehydrogenases active site. S-N-H-G-[AG]-R-Q
source prosite : PS00557

45) chain A
residue 39-46
type prosite
ligand
sequence FLPNHPGG
description Cytochrome b5 family, heme-binding domain signature. [FY]-[LIVMK]-{I}-{Q}-H-P-[GA]-G
source prosite : PS00191

46) chain A
residue 27
type binding
ligand HEM: PROTOPORPHYRIN IX CONTAINING FE
sequence V
description PROTOPORPHYRIN IX CONTAINING FE binding site
source pdb_hetatom : HEM_1ldc_A_560

47) chain A
residue 29
type binding
ligand HEM: PROTOPORPHYRIN IX CONTAINING FE
sequence I
description PROTOPORPHYRIN IX CONTAINING FE binding site
source pdb_hetatom : HEM_1ldc_A_560

48) chain A
residue 36
type binding
ligand HEM: PROTOPORPHYRIN IX CONTAINING FE
sequence L
description PROTOPORPHYRIN IX CONTAINING FE binding site
source pdb_hetatom : HEM_1ldc_A_560

49) chain A
residue 39
type binding
ligand HEM: PROTOPORPHYRIN IX CONTAINING FE
sequence F
description PROTOPORPHYRIN IX CONTAINING FE binding site
source pdb_hetatom : HEM_1ldc_A_560

50) chain A
residue 43-45
type binding
ligand HEM: PROTOPORPHYRIN IX CONTAINING FE
sequence HPG
description PROTOPORPHYRIN IX CONTAINING FE binding site
source pdb_hetatom : HEM_1ldc_A_560

51) chain A
residue 49-50
type binding
ligand HEM: PROTOPORPHYRIN IX CONTAINING FE
sequence VI
description PROTOPORPHYRIN IX CONTAINING FE binding site
source pdb_hetatom : HEM_1ldc_A_560

52) chain A
residue 53
type binding
ligand HEM: PROTOPORPHYRIN IX CONTAINING FE
sequence N
description PROTOPORPHYRIN IX CONTAINING FE binding site
source pdb_hetatom : HEM_1ldc_A_560

53) chain A
residue 58
type binding
ligand HEM: PROTOPORPHYRIN IX CONTAINING FE
sequence V
description PROTOPORPHYRIN IX CONTAINING FE binding site
source pdb_hetatom : HEM_1ldc_A_560

54) chain A
residue 61-62
type binding
ligand HEM: PROTOPORPHYRIN IX CONTAINING FE
sequence IF
description PROTOPORPHYRIN IX CONTAINING FE binding site
source pdb_hetatom : HEM_1ldc_A_560

55) chain A
residue 65-66
type binding
ligand HEM: PROTOPORPHYRIN IX CONTAINING FE
sequence LH
description PROTOPORPHYRIN IX CONTAINING FE binding site
source pdb_hetatom : HEM_1ldc_A_560

56) chain A
residue 70-71
type binding
ligand HEM: PROTOPORPHYRIN IX CONTAINING FE
sequence VI
description PROTOPORPHYRIN IX CONTAINING FE binding site
source pdb_hetatom : HEM_1ldc_A_560

57) chain A
residue 74-75
type binding
ligand HEM: PROTOPORPHYRIN IX CONTAINING FE
sequence YI
description PROTOPORPHYRIN IX CONTAINING FE binding site
source pdb_hetatom : HEM_1ldc_A_560

58) chain A
residue 97
type binding
ligand HEM: PROTOPORPHYRIN IX CONTAINING FE
sequence Y
description PROTOPORPHYRIN IX CONTAINING FE binding site
source pdb_hetatom : HEM_1ldc_A_560

59) chain A
residue 139
type binding
ligand HEM: PROTOPORPHYRIN IX CONTAINING FE
sequence Q
description PROTOPORPHYRIN IX CONTAINING FE binding site
source pdb_hetatom : HEM_1ldc_A_560

60) chain A
residue 143
type binding
ligand HEM: PROTOPORPHYRIN IX CONTAINING FE
sequence F
description PROTOPORPHYRIN IX CONTAINING FE binding site
source pdb_hetatom : HEM_1ldc_A_560

61) chain A
residue 198-199
type binding
ligand HEM: PROTOPORPHYRIN IX CONTAINING FE
sequence AL
description PROTOPORPHYRIN IX CONTAINING FE binding site
source pdb_hetatom : HEM_1ldc_A_560

62) chain A
residue 230
type binding
ligand HEM: PROTOPORPHYRIN IX CONTAINING FE
sequence L
description PROTOPORPHYRIN IX CONTAINING FE binding site
source pdb_hetatom : HEM_1ldc_A_560

63) chain A
residue 289
type binding
ligand HEM: PROTOPORPHYRIN IX CONTAINING FE
sequence R
description PROTOPORPHYRIN IX CONTAINING FE binding site
source pdb_hetatom : HEM_1ldc_A_560

64) chain A
residue 292
type binding
ligand HEM: PROTOPORPHYRIN IX CONTAINING FE
sequence D
description PROTOPORPHYRIN IX CONTAINING FE binding site
source pdb_hetatom : HEM_1ldc_A_560

65) chain A
residue 296
type binding
ligand HEM: PROTOPORPHYRIN IX CONTAINING FE
sequence K
description PROTOPORPHYRIN IX CONTAINING FE binding site
source pdb_hetatom : HEM_1ldc_A_560

66) chain A
residue 325
type binding
ligand HEM: PROTOPORPHYRIN IX CONTAINING FE
sequence F
description PROTOPORPHYRIN IX CONTAINING FE binding site
source pdb_hetatom : HEM_1ldc_A_560

67) chain A
residue 143-144
type binding
ligand FMN: FLAVIN MONONUCLEOTIDE
sequence FY
description FLAVIN MONONUCLEOTIDE binding site
source pdb_hetatom : FMN_1ldc_A_570

68) chain A
residue 154
type binding
ligand FMN: FLAVIN MONONUCLEOTIDE
sequence H
description FLAVIN MONONUCLEOTIDE binding site
source pdb_hetatom : FMN_1ldc_A_570

69) chain A
residue 195-198
type binding
ligand FMN: FLAVIN MONONUCLEOTIDE
sequence SATA
description FLAVIN MONONUCLEOTIDE binding site
source pdb_hetatom : FMN_1ldc_A_570

70) chain A
residue 226
type binding
ligand FMN: FLAVIN MONONUCLEOTIDE
sequence M
description FLAVIN MONONUCLEOTIDE binding site
source pdb_hetatom : FMN_1ldc_A_570

71) chain A
residue 228-230
type binding
ligand FMN: FLAVIN MONONUCLEOTIDE
sequence STL
description FLAVIN MONONUCLEOTIDE binding site
source pdb_hetatom : FMN_1ldc_A_570

72) chain A
residue 252
type binding
ligand FMN: FLAVIN MONONUCLEOTIDE
sequence Q
description FLAVIN MONONUCLEOTIDE binding site
source pdb_hetatom : FMN_1ldc_A_570

73) chain A
residue 254
type binding
ligand FMN: FLAVIN MONONUCLEOTIDE
sequence Y
description FLAVIN MONONUCLEOTIDE binding site
source pdb_hetatom : FMN_1ldc_A_570

74) chain A
residue 280
type binding
ligand FMN: FLAVIN MONONUCLEOTIDE
sequence T
description FLAVIN MONONUCLEOTIDE binding site
source pdb_hetatom : FMN_1ldc_A_570

75) chain A
residue 289
type binding
ligand FMN: FLAVIN MONONUCLEOTIDE
sequence R
description FLAVIN MONONUCLEOTIDE binding site
source pdb_hetatom : FMN_1ldc_A_570

76) chain A
residue 349
type binding
ligand FMN: FLAVIN MONONUCLEOTIDE
sequence K
description FLAVIN MONONUCLEOTIDE binding site
source pdb_hetatom : FMN_1ldc_A_570

77) chain A
residue 371
type binding
ligand FMN: FLAVIN MONONUCLEOTIDE
sequence S
description FLAVIN MONONUCLEOTIDE binding site
source pdb_hetatom : FMN_1ldc_A_570

78) chain A
residue 373-374
type binding
ligand FMN: FLAVIN MONONUCLEOTIDE
sequence HG
description FLAVIN MONONUCLEOTIDE binding site
source pdb_hetatom : FMN_1ldc_A_570

79) chain A
residue 376
type binding
ligand FMN: FLAVIN MONONUCLEOTIDE
sequence R
description FLAVIN MONONUCLEOTIDE binding site
source pdb_hetatom : FMN_1ldc_A_570

80) chain A
residue 409-413
type binding
ligand FMN: FLAVIN MONONUCLEOTIDE
sequence DGGVR
description FLAVIN MONONUCLEOTIDE binding site
source pdb_hetatom : FMN_1ldc_A_570

81) chain A
residue 430-434
type binding
ligand FMN: FLAVIN MONONUCLEOTIDE
sequence GLGRP
description FLAVIN MONONUCLEOTIDE binding site
source pdb_hetatom : FMN_1ldc_A_570

82) chain A
residue 436
type binding
ligand FMN: FLAVIN MONONUCLEOTIDE
sequence L
description FLAVIN MONONUCLEOTIDE binding site
source pdb_hetatom : FMN_1ldc_A_570

83) chain A
residue 143
type binding
ligand PYR: PYRUVIC ACID
sequence F
description PYRUVIC ACID binding site
source pdb_hetatom : PYR_1ldc_A_580

84) chain A
residue 198
type binding
ligand PYR: PYRUVIC ACID
sequence A
description PYRUVIC ACID binding site
source pdb_hetatom : PYR_1ldc_A_580

85) chain A
residue 230
type binding
ligand PYR: PYRUVIC ACID
sequence L
description PYRUVIC ACID binding site
source pdb_hetatom : PYR_1ldc_A_580

86) chain A
residue 254
type binding
ligand PYR: PYRUVIC ACID
sequence Y
description PYRUVIC ACID binding site
source pdb_hetatom : PYR_1ldc_A_580

87) chain A
residue 286
type binding
ligand PYR: PYRUVIC ACID
sequence L
description PYRUVIC ACID binding site
source pdb_hetatom : PYR_1ldc_A_580

88) chain A
residue 289
type binding
ligand PYR: PYRUVIC ACID
sequence R
description PYRUVIC ACID binding site
source pdb_hetatom : PYR_1ldc_A_580

89) chain A
residue 373
type binding
ligand PYR: PYRUVIC ACID
sequence H
description PYRUVIC ACID binding site
source pdb_hetatom : PYR_1ldc_A_580

90) chain A
residue 376
type binding
ligand PYR: PYRUVIC ACID
sequence R
description PYRUVIC ACID binding site
source pdb_hetatom : PYR_1ldc_A_580

91) chain A
residue 254
type catalytic
ligand
sequence Y
description Annotated By Reference To The Literature 1fcb
source CSA : CSA1

92) chain A
residue 143
type catalytic
ligand
sequence F
description Annotated By Reference To The Literature 1fcb
source CSA : CSA1

93) chain A
residue 376
type catalytic
ligand
sequence R
description Annotated By Reference To The Literature 1fcb
source CSA : CSA1

94) chain A
residue 282
type catalytic
ligand
sequence D
description Annotated By Reference To The Literature 1fcb
source CSA : CSA1

95) chain A
residue 373
type catalytic
ligand
sequence H
description Annotated By Reference To The Literature 1fcb
source CSA : CSA1

96) chain A
residue 254
type catalytic
ligand
sequence Y
description Annotated By Reference To The Literature 1fcb
source CSA : CSA3

97) chain A
residue 376
type catalytic
ligand
sequence R
description Annotated By Reference To The Literature 1fcb
source CSA : CSA3

98) chain A
residue 373
type catalytic
ligand
sequence H
description Annotated By Reference To The Literature 1fcb
source CSA : CSA3

99) chain A
residue 282
type catalytic
ligand
sequence D
description Annotated By Reference To The Literature 1fcb
source CSA : CSA3


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