PDB entry 4zda

View 4zda on RCSB PDB site
Description: Crystal structure of isocitrate dehydrogenase in complex with isocitrate and Mn from M. smegmatis
Class: oxidoreductase
Keywords: ICD, M. smegmatis, complex, Isocitrate, OXIDOREDUCTASE
Deposited on 2015-04-17, released 2016-06-29
The last revision prior to the SCOPe 2.07 freeze date was dated 2016-06-29, with a file datestamp of 2016-06-24.
Experiment type: XRAY
Resolution: 2.8 Å
R-factor: N/A
AEROSPACI score: 0.16 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: Isocitrate dehydrogenase (NADP) Icd2
    Species: Mycobacterium smegmatis [TaxId:1772]
    Gene: icd2, MSMEG_1654, MSMEI_1615
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d4zdaa_
  • Chain 'B':
    Compound: Isocitrate dehydrogenase (NADP) Icd2
    Species: Mycobacterium smegmatis [TaxId:1772]
    Gene: icd2, MSMEG_1654, MSMEI_1615
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d4zdab_
  • Chain 'C':
    Compound: Isocitrate dehydrogenase (NADP) Icd2
    Species: Mycobacterium smegmatis [TaxId:1772]
    Gene: icd2, MSMEG_1654, MSMEI_1615
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d4zdac_
  • Chain 'D':
    Compound: Isocitrate dehydrogenase (NADP) Icd2
    Species: Mycobacterium smegmatis [TaxId:1772]
    Gene: icd2, MSMEG_1654, MSMEI_1615
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d4zdad_
  • Chain 'E':
    Compound: Isocitrate dehydrogenase (NADP) Icd2
    Species: Mycobacterium smegmatis [TaxId:1772]
    Gene: icd2, MSMEG_1654, MSMEI_1615
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d4zdae_
  • Chain 'F':
    Compound: Isocitrate dehydrogenase (NADP) Icd2
    Species: Mycobacterium smegmatis [TaxId:1772]
    Gene: icd2, MSMEG_1654, MSMEI_1615
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d4zdaf_
  • Heterogens: MN, ICT

PDB Chain Sequences:

  • Chain 'A':
    Sequence, based on SEQRES records: (download) 
    >4zdaA (A:)
msaqqptiiytltdeapllatyaflpvvrkfaeaagidvktsdisvaarilaefgdhlte
eqrvpdnlgelgaltqdpsaniiklpnisasvpqllaaikelqgkgynvpdypanpktdd
ekkikdryakilgsavnpvlregnsdrrapkavkeyarkhphsmgewsqasrthvatmkt
gdfyhgeksmtldrdrrvkmvlktksgeeivlkpevkldagdiidsmymskkaliafyee
qiedayktgvmfslhvkatmmkvshpivfghavkvfykdafakheklfdelgvnvnngls
dlydkiealpasqreeiiedlhkchehrpelamvdsakgisnfhspsdvivdasmpamir
lggkmygadgrtkdtkavnpestfsrmyqeminfckthgqfdpttmgtvpnvglmaqkae
eygshdktfeipedgvadivdidtgevlltqnveegdiwrmpivkdapirdwvklavtra
rlsgmpvvfwldterphevelrkkvkeylkdhdteglkiqimpqvwamrytlervvrgkd
tiaatgnilrdyltdlfpilelgtsakmlsivplmaggglyetgaggsapkhvhqlveen
hlrwdslgeflalgasledmgnktgnekakvlakaldtatgklleenkspsrrtgeldnr
gsqfylslfwaqalaeqtedaelaerfkplakalaeqeeaivselnsvqgktvdiggyyy
pdpektsevmrpsktfnttlesvprypydvpdyaklaaalehhhhhh

    Sequence, based on observed residues (ATOM records): (download) 
    >4zdaA (A:)
ptiiytltdeapllatyaflpvvrkfaeaagidvktsdisvaarilaefgdhlteeqrvp
dnlgelgaltqdpsaniiklpnisasvpqllaaikelqgkgynvpdypanpktddekkik
dryakilgsavnpvlregnsdrrapkavkeyarkhphsmgewsqasrthvatmktgdfyh
geksmtldrdrrvkmvlktksgeeivlkpevkldagdiidsmymskkaliafyeeqieda
yktgvmfslhvkatmmkvshpivfghavkvfykdafakheklfdelgvnvnnglsdlydk
iealpasqreeiiedlhkchehrpelamvdsakgisnfhspsdvivdasmpamirlggkm
ygadgrtkdtkavnpestfsrmyqeminfckthgqfdpttmgtvpnvglmaqkaeeygsh
dktfeipedgvadivdidtgevlltqnveegdiwrmpivkdapirdwvklavtrarlsgm
pvvfwldterphevelrkkvkeylkdhdteglkiqimpqvwamrytlervvrgkdtiaat
gnilrdyltdlfpilelgtsakmlsivplmaggglyetgaggsapkhvhqlveenhlrwd
slgeflalgasledmgnktgnekakvlakaldtatgklleenkspsrrtgeldnrgsqfy
lslfwaqalaeqtedaelaerfkplakalaeqeeaivselnsvqgktvdiggyyypdpek
tsevmrpsktfnttl

  • Chain 'B':
    Sequence, based on SEQRES records: (download) 
    >4zdaB (B:)
msaqqptiiytltdeapllatyaflpvvrkfaeaagidvktsdisvaarilaefgdhlte
eqrvpdnlgelgaltqdpsaniiklpnisasvpqllaaikelqgkgynvpdypanpktdd
ekkikdryakilgsavnpvlregnsdrrapkavkeyarkhphsmgewsqasrthvatmkt
gdfyhgeksmtldrdrrvkmvlktksgeeivlkpevkldagdiidsmymskkaliafyee
qiedayktgvmfslhvkatmmkvshpivfghavkvfykdafakheklfdelgvnvnngls
dlydkiealpasqreeiiedlhkchehrpelamvdsakgisnfhspsdvivdasmpamir
lggkmygadgrtkdtkavnpestfsrmyqeminfckthgqfdpttmgtvpnvglmaqkae
eygshdktfeipedgvadivdidtgevlltqnveegdiwrmpivkdapirdwvklavtra
rlsgmpvvfwldterphevelrkkvkeylkdhdteglkiqimpqvwamrytlervvrgkd
tiaatgnilrdyltdlfpilelgtsakmlsivplmaggglyetgaggsapkhvhqlveen
hlrwdslgeflalgasledmgnktgnekakvlakaldtatgklleenkspsrrtgeldnr
gsqfylslfwaqalaeqtedaelaerfkplakalaeqeeaivselnsvqgktvdiggyyy
pdpektsevmrpsktfnttlesvprypydvpdyaklaaalehhhhhh

    Sequence, based on observed residues (ATOM records): (download) 
    >4zdaB (B:)
ptiiytltdeapllatyaflpvvrkfaeaagidvktsdisvaarilaefgdhlteeqrvp
dnlgelgaltqdpsaniiklpnisasvpqllaaikelqgkgynvpdypanpktddekkik
dryakilgsavnpvlregnsdrrapkavkeyarkhphsmgewsqasrthvatmktgdfyh
geksmtldrdrrvkmvlktksgeeivlkpevkldagdiidsmymskkaliafyeeqieda
yktgvmfslhvkatmmkvshpivfghavkvfykdafakheklfdelgvnvnnglsdlydk
iealpasqreeiiedlhkchehrpelamvdsakgisnfhspsdvivdasmpamirlggkm
ygadgrtkdtkavnpestfsrmyqeminfckthgqfdpttmgtvpnvglmaqkaeeygsh
dktfeipedgvadivdidtgevlltqnveegdiwrmpivkdapirdwvklavtrarlsgm
pvvfwldterphevelrkkvkeylkdhdteglkiqimpqvwamrytlervvrgkdtiaat
gnilrdyltdlfpilelgtsakmlsivplmaggglyetgaggsapkhvhqlveenhlrwd
slgeflalgasledmgnktgnekakvlakaldtatgklleenkspsrrtgeldnrgsqfy
lslfwaqalaeqtedaelaerfkplakalaeqeeaivselnsvqgktvdiggyyypdpek
tsevmrpsktfnttl

  • Chain 'C':
    Sequence, based on SEQRES records: (download) 
    >4zdaC (C:)
msaqqptiiytltdeapllatyaflpvvrkfaeaagidvktsdisvaarilaefgdhlte
eqrvpdnlgelgaltqdpsaniiklpnisasvpqllaaikelqgkgynvpdypanpktdd
ekkikdryakilgsavnpvlregnsdrrapkavkeyarkhphsmgewsqasrthvatmkt
gdfyhgeksmtldrdrrvkmvlktksgeeivlkpevkldagdiidsmymskkaliafyee
qiedayktgvmfslhvkatmmkvshpivfghavkvfykdafakheklfdelgvnvnngls
dlydkiealpasqreeiiedlhkchehrpelamvdsakgisnfhspsdvivdasmpamir
lggkmygadgrtkdtkavnpestfsrmyqeminfckthgqfdpttmgtvpnvglmaqkae
eygshdktfeipedgvadivdidtgevlltqnveegdiwrmpivkdapirdwvklavtra
rlsgmpvvfwldterphevelrkkvkeylkdhdteglkiqimpqvwamrytlervvrgkd
tiaatgnilrdyltdlfpilelgtsakmlsivplmaggglyetgaggsapkhvhqlveen
hlrwdslgeflalgasledmgnktgnekakvlakaldtatgklleenkspsrrtgeldnr
gsqfylslfwaqalaeqtedaelaerfkplakalaeqeeaivselnsvqgktvdiggyyy
pdpektsevmrpsktfnttlesvprypydvpdyaklaaalehhhhhh

    Sequence, based on observed residues (ATOM records): (download) 
    >4zdaC (C:)
ptiiytltdeapllatyaflpvvrkfaeaagidvktsdisvaarilaefgdhlteeqrvp
dnlgelgaltqdpsaniiklpnisasvpqllaaikelqgkgynvpdypanpktddekkik
dryakilgsavnpvlregnsdrrapkavkeyarkhphsmgewsqasrthvatmktgdfyh
geksmtldrdrrvkmvlktksgeeivlkpevkldagdiidsmymskkaliafyeeqieda
yktgvmfslhvkatmmkvshpivfghavkvfykdafakheklfdelgvnvnnglsdlydk
iealpasqreeiiedlhkchehrpelamvdsakgisnfhspsdvivdasmpamirlggkm
ygadgrtkdtkavnpestfsrmyqeminfckthgqfdpttmgtvpnvglmaqkaeeygsh
dktfeipedgvadivdidtgevlltqnveegdiwrmpivkdapirdwvklavtrarlsgm
pvvfwldterphevelrkkvkeylkdhdteglkiqimpqvwamrytlervvrgkdtiaat
gnilrdyltdlfpilelgtsakmlsivplmaggglyetgaggsapkhvhqlveenhlrwd
slgeflalgasledmgnktgnekakvlakaldtatgklleenkspsrrtgeldnrgsqfy
lslfwaqalaeqtedaelaerfkplakalaeqeeaivselnsvqgktvdiggyyypdpek
tsevmrpsktfnttl

  • Chain 'D':
    Sequence, based on SEQRES records: (download) 
    >4zdaD (D:)
msaqqptiiytltdeapllatyaflpvvrkfaeaagidvktsdisvaarilaefgdhlte
eqrvpdnlgelgaltqdpsaniiklpnisasvpqllaaikelqgkgynvpdypanpktdd
ekkikdryakilgsavnpvlregnsdrrapkavkeyarkhphsmgewsqasrthvatmkt
gdfyhgeksmtldrdrrvkmvlktksgeeivlkpevkldagdiidsmymskkaliafyee
qiedayktgvmfslhvkatmmkvshpivfghavkvfykdafakheklfdelgvnvnngls
dlydkiealpasqreeiiedlhkchehrpelamvdsakgisnfhspsdvivdasmpamir
lggkmygadgrtkdtkavnpestfsrmyqeminfckthgqfdpttmgtvpnvglmaqkae
eygshdktfeipedgvadivdidtgevlltqnveegdiwrmpivkdapirdwvklavtra
rlsgmpvvfwldterphevelrkkvkeylkdhdteglkiqimpqvwamrytlervvrgkd
tiaatgnilrdyltdlfpilelgtsakmlsivplmaggglyetgaggsapkhvhqlveen
hlrwdslgeflalgasledmgnktgnekakvlakaldtatgklleenkspsrrtgeldnr
gsqfylslfwaqalaeqtedaelaerfkplakalaeqeeaivselnsvqgktvdiggyyy
pdpektsevmrpsktfnttlesvprypydvpdyaklaaalehhhhhh

    Sequence, based on observed residues (ATOM records): (download) 
    >4zdaD (D:)
ptiiytltdeapllatyaflpvvrkfaeaagidvktsdisvaarilaefgdhlteeqrvp
dnlgelgaltqdpsaniiklpnisasvpqllaaikelqgkgynvpdypanpktddekkik
dryakilgsavnpvlregnsdrrapkavkeyarkhphsmgewsqasrthvatmktgdfyh
geksmtldrdrrvkmvlktksgeeivlkpevkldagdiidsmymskkaliafyeeqieda
yktgvmfslhvkatmmkvshpivfghavkvfykdafakheklfdelgvnvnnglsdlydk
iealpasqreeiiedlhkchehrpelamvdsakgisnfhspsdvivdasmpamirlggkm
ygadgrtkdtkavnpestfsrmyqeminfckthgqfdpttmgtvpnvglmaqkaeeygsh
dktfeipedgvadivdidtgevlltqnveegdiwrmpivkdapirdwvklavtrarlsgm
pvvfwldterphevelrkkvkeylkdhdteglkiqimpqvwamrytlervvrgkdtiaat
gnilrdyltdlfpilelgtsakmlsivplmaggglyetgaggsapkhvhqlveenhlrwd
slgeflalgasledmgnktgnekakvlakaldtatgklleenkspsrrtgeldnrgsqfy
lslfwaqalaeqtedaelaerfkplakalaeqeeaivselnsvqgktvdiggyyypdpek
tsevmrpsktfnttl

  • Chain 'E':
    Sequence, based on SEQRES records: (download) 
    >4zdaE (E:)
msaqqptiiytltdeapllatyaflpvvrkfaeaagidvktsdisvaarilaefgdhlte
eqrvpdnlgelgaltqdpsaniiklpnisasvpqllaaikelqgkgynvpdypanpktdd
ekkikdryakilgsavnpvlregnsdrrapkavkeyarkhphsmgewsqasrthvatmkt
gdfyhgeksmtldrdrrvkmvlktksgeeivlkpevkldagdiidsmymskkaliafyee
qiedayktgvmfslhvkatmmkvshpivfghavkvfykdafakheklfdelgvnvnngls
dlydkiealpasqreeiiedlhkchehrpelamvdsakgisnfhspsdvivdasmpamir
lggkmygadgrtkdtkavnpestfsrmyqeminfckthgqfdpttmgtvpnvglmaqkae
eygshdktfeipedgvadivdidtgevlltqnveegdiwrmpivkdapirdwvklavtra
rlsgmpvvfwldterphevelrkkvkeylkdhdteglkiqimpqvwamrytlervvrgkd
tiaatgnilrdyltdlfpilelgtsakmlsivplmaggglyetgaggsapkhvhqlveen
hlrwdslgeflalgasledmgnktgnekakvlakaldtatgklleenkspsrrtgeldnr
gsqfylslfwaqalaeqtedaelaerfkplakalaeqeeaivselnsvqgktvdiggyyy
pdpektsevmrpsktfnttlesvprypydvpdyaklaaalehhhhhh

    Sequence, based on observed residues (ATOM records): (download) 
    >4zdaE (E:)
ptiiytltdeapllatyaflpvvrkfaeaagidvktsdisvaarilaefgdhlteeqrvp
dnlgelgaltqdpsaniiklpnisasvpqllaaikelqgkgynvpdypanpktddekkik
dryakilgsavnpvlregnsdrrapkavkeyarkhphsmgewsqasrthvatmktgdfyh
geksmtldrdrrvkmvlktksgeeivlkpevkldagdiidsmymskkaliafyeeqieda
yktgvmfslhvkatmmkvshpivfghavkvfykdafakheklfdelgvnvnnglsdlydk
iealpasqreeiiedlhkchehrpelamvdsakgisnfhspsdvivdasmpamirlggkm
ygadgrtkdtkavnpestfsrmyqeminfckthgqfdpttmgtvpnvglmaqkaeeygsh
dktfeipedgvadivdidtgevlltqnveegdiwrmpivkdapirdwvklavtrarlsgm
pvvfwldterphevelrkkvkeylkdhdteglkiqimpqvwamrytlervvrgkdtiaat
gnilrdyltdlfpilelgtsakmlsivplmaggglyetgaggsapkhvhqlveenhlrwd
slgeflalgasledmgnktgnekakvlakaldtatgklleenkspsrrtgeldnrgsqfy
lslfwaqalaeqtedaelaerfkplakalaeqeeaivselnsvqgktvdiggyyypdpek
tsevmrpsktfnttl

  • Chain 'F':
    Sequence, based on SEQRES records: (download) 
    >4zdaF (F:)
msaqqptiiytltdeapllatyaflpvvrkfaeaagidvktsdisvaarilaefgdhlte
eqrvpdnlgelgaltqdpsaniiklpnisasvpqllaaikelqgkgynvpdypanpktdd
ekkikdryakilgsavnpvlregnsdrrapkavkeyarkhphsmgewsqasrthvatmkt
gdfyhgeksmtldrdrrvkmvlktksgeeivlkpevkldagdiidsmymskkaliafyee
qiedayktgvmfslhvkatmmkvshpivfghavkvfykdafakheklfdelgvnvnngls
dlydkiealpasqreeiiedlhkchehrpelamvdsakgisnfhspsdvivdasmpamir
lggkmygadgrtkdtkavnpestfsrmyqeminfckthgqfdpttmgtvpnvglmaqkae
eygshdktfeipedgvadivdidtgevlltqnveegdiwrmpivkdapirdwvklavtra
rlsgmpvvfwldterphevelrkkvkeylkdhdteglkiqimpqvwamrytlervvrgkd
tiaatgnilrdyltdlfpilelgtsakmlsivplmaggglyetgaggsapkhvhqlveen
hlrwdslgeflalgasledmgnktgnekakvlakaldtatgklleenkspsrrtgeldnr
gsqfylslfwaqalaeqtedaelaerfkplakalaeqeeaivselnsvqgktvdiggyyy
pdpektsevmrpsktfnttlesvprypydvpdyaklaaalehhhhhh

    Sequence, based on observed residues (ATOM records): (download) 
    >4zdaF (F:)
ptiiytltdeapllatyaflpvvrkfaeaagidvktsdisvaarilaefgdhlteeqrvp
dnlgelgaltqdpsaniiklpnisasvpqllaaikelqgkgynvpdypanpktddekkik
dryakilgsavnpvlregnsdrrapkavkeyarkhphsmgewsqasrthvatmktgdfyh
geksmtldrdrrvkmvlktksgeeivlkpevkldagdiidsmymskkaliafyeeqieda
yktgvmfslhvkatmmkvshpivfghavkvfykdafakheklfdelgvnvnnglsdlydk
iealpasqreeiiedlhkchehrpelamvdsakgisnfhspsdvivdasmpamirlggkm
ygadgrtkdtkavnpestfsrmyqeminfckthgqfdpttmgtvpnvglmaqkaeeygsh
dktfeipedgvadivdidtgevlltqnveegdiwrmpivkdapirdwvklavtrarlsgm
pvvfwldterphevelrkkvkeylkdhdteglkiqimpqvwamrytlervvrgkdtiaat
gnilrdyltdlfpilelgtsakmlsivplmaggglyetgaggsapkhvhqlveenhlrwd
slgeflalgasledmgnktgnekakvlakaldtatgklleenkspsrrtgeldnrgsqfy
lslfwaqalaeqtedaelaerfkplakalaeqeeaivselnsvqgktvdiggyyypdpek
tsevmrpsktfnttl