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

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Title STRUCTURE OF ISOCITRATE DEHYDROGENASE WITH ALPHA-KETOGLUTARATE AT 2.7 ANGSTROMS RESOLUTION: CONFORMATIONAL CHANGES INDUCED BY DECARBOXYLATION OF ISOCITRATE
Classification OXIDOREDUCTASE(NAD(A)-CHOH(D))
Compound ISOCITRATE DEHYDROGENASE
Source Escherichia coli (strain K12) (IDH_ECOLI)
Sequence A:  SKVVVPAQGKKITLQNGKLNVPENPIIPYIEGDGIGVDVT
PAMLKVVDAAVEKAYKGERKISWMEIYTGEKSTQVYGQDV
WLPAETLDLIREYRVAIKGPLTTPVGGGIRSLNVALRQEL
DLYICLRPVRYYQGTPSPVKHPELTDMVIFRENSEDIYAG
IEWKADSADAEKVIKFLREEMGVKKIRFPEHCGIGIKPCS
EEGTKRLVRAAIEYAIANDRDSVTLVHKGNIMKFTEGAFK
DWGYQLAREEFGGELIDGGPWLKVKNPNTGKEIVIKDVIA
DAFLQQILLRPAEYDVIACMNLNGDYISDALAAQVGGIGI
APGANIGDECALFEATHGTAPKYAGQDKVNPGSIILSAEM
MLRHMGWTEAADLIVKGMEGAINAKTVTYDFERLMDGAKL
LKCSEFGDAIIENM
Description (1)  ISOCITRATE DEHYDROGENASE (E.C.1.1.1.42) COMPLEXED WITH ALPHA-KETOGLUTARATE


Functional site

1) chain A
residue 307
type
ligand
sequence D
description BINDING SITE FOR RESIDUE CA A 417
source : AC1

2) chain A
residue 311
type
ligand
sequence D
description BINDING SITE FOR RESIDUE CA A 417
source : AC1

3) chain A
residue 113
type
ligand
sequence S
description BINDING SITE FOR RESIDUE AKG A 418
source : AC2

4) chain A
residue 115
type
ligand
sequence N
description BINDING SITE FOR RESIDUE AKG A 418
source : AC2

5) chain A
residue 119
type
ligand
sequence R
description BINDING SITE FOR RESIDUE AKG A 418
source : AC2

6) chain A
residue 129
type
ligand
sequence R
description BINDING SITE FOR RESIDUE AKG A 418
source : AC2

7) chain A
residue 230
type
ligand
sequence K
description BINDING SITE FOR RESIDUE AKG A 418
source : AC2

8) chain A
residue 283
type
ligand
sequence D
description BINDING SITE FOR RESIDUE AKG A 418
source : AC2

9) chain A
residue 307
type
ligand
sequence D
description BINDING SITE FOR RESIDUE AKG A 418
source : AC2

10) chain A
residue 311
type
ligand
sequence D
description BINDING SITE FOR RESIDUE AKG A 418
source : AC2

11) chain A
residue 307
type METAL
ligand
sequence D
description Magnesium or manganese
source Swiss-Prot : SWS_FT_FI1

12) chain A
residue 352
type BINDING
ligand
sequence N
description NADP; via amide nitrogen and carbonyl oxygen.
source Swiss-Prot : SWS_FT_FI2

13) chain A
residue 113
type BINDING
ligand
sequence S
description Substrate.
source Swiss-Prot : SWS_FT_FI3

14) chain A
residue 115
type BINDING
ligand
sequence N
description Substrate.
source Swiss-Prot : SWS_FT_FI3

15) chain A
residue 119
type BINDING
ligand
sequence R
description Substrate.
source Swiss-Prot : SWS_FT_FI3

16) chain A
residue 129
type BINDING
ligand
sequence R
description Substrate.
source Swiss-Prot : SWS_FT_FI3

17) chain A
residue 153
type BINDING
ligand
sequence R
description Substrate.
source Swiss-Prot : SWS_FT_FI3

18) chain A
residue 104
type BINDING
ligand
sequence T
description NADP.
source Swiss-Prot : SWS_FT_FI4

19) chain A
residue 391
type BINDING
ligand
sequence Y
description NADP.
source Swiss-Prot : SWS_FT_FI4

20) chain A
residue 395
type BINDING
ligand
sequence R
description NADP.
source Swiss-Prot : SWS_FT_FI4

21) chain A
residue 160
type SITE
ligand
sequence Y
description Critical for catalysis.
source Swiss-Prot : SWS_FT_FI5

22) chain A
residue 230
type SITE
ligand
sequence K
description Critical for catalysis.
source Swiss-Prot : SWS_FT_FI5

23) chain A
residue 339-345
type NP_BIND
ligand
sequence HGTAPKY
description NADP.
source Swiss-Prot : SWS_FT_FI6

24) chain A
residue 140
type catalytic
ligand
sequence P
description Mapped from 1a05 to 1ika using BLAST. All catalytic residues present. Original details record follows: a catalytic site defined by CATRES, Medline 91363356, 94009683, 94188357, 94330710, 95119012
source extCATRES : extCATRES1

25) chain A
residue 303-322
type prosite
ligand
sequence NLNGDYISDALAAQVGGIGI
description Isocitrate and isopropylmalate dehydrogenases signature. [NSK]-[LIMYTV]-[FYDNH]-[GEA]-[DNGSTY]-[IMVYL]-x-[STGDN]-[DN]-x(1,2)
source prosite : PS00470

26) chain A
residue 113
type binding
ligand AKG: 2-OXOGLUTARIC ACID
sequence S
description 2-OXOGLUTARIC ACID binding site
source pdb_hetatom : AKG_1ika_A_418

27) chain A
residue 115
type binding
ligand AKG: 2-OXOGLUTARIC ACID
sequence N
description 2-OXOGLUTARIC ACID binding site
source pdb_hetatom : AKG_1ika_A_418

28) chain A
residue 119
type binding
ligand AKG: 2-OXOGLUTARIC ACID
sequence R
description 2-OXOGLUTARIC ACID binding site
source pdb_hetatom : AKG_1ika_A_418

29) chain A
residue 129
type binding
ligand AKG: 2-OXOGLUTARIC ACID
sequence R
description 2-OXOGLUTARIC ACID binding site
source pdb_hetatom : AKG_1ika_A_418

30) chain A
residue 153
type binding
ligand AKG: 2-OXOGLUTARIC ACID
sequence R
description 2-OXOGLUTARIC ACID binding site
source pdb_hetatom : AKG_1ika_A_418

31) chain A
residue 307
type binding
ligand AKG: 2-OXOGLUTARIC ACID
sequence D
description 2-OXOGLUTARIC ACID binding site
source pdb_hetatom : AKG_1ika_A_418

32) chain A
residue 311
type binding
ligand AKG: 2-OXOGLUTARIC ACID
sequence D
description 2-OXOGLUTARIC ACID binding site
source pdb_hetatom : AKG_1ika_A_418

33) chain A
residue 338
type binding
ligand AKG: 2-OXOGLUTARIC ACID
sequence T
description 2-OXOGLUTARIC ACID binding site
source pdb_hetatom : AKG_1ika_A_418

34) chain A
residue 160
type catalytic
ligand
sequence Y
description Annotated By Reference To The Literature 1a05
source CSA : CSA1

35) chain A
residue 283
type catalytic
ligand
sequence D
description Annotated By Reference To The Literature 1a05
source CSA : CSA2

36) chain A
residue 230
type catalytic
ligand
sequence K
description Annotated By Reference To The Literature 1a05
source CSA : CSA2


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