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6C4A

Crystal structure of 3-nitropropionate modified isocitrate lyase from Mycobacterium tuberculosis with pyruvate

Functional Information from GO Data
ChainGOidnamespacecontents
A0003824molecular_functioncatalytic activity
A0004451molecular_functionisocitrate lyase activity
A0005576cellular_componentextracellular region
A0005829cellular_componentcytosol
A0005886cellular_componentplasma membrane
A0006097biological_processglyoxylate cycle
A0006099biological_processtricarboxylic acid cycle
A0006102biological_processisocitrate metabolic process
A0016829molecular_functionlyase activity
A0019752biological_processcarboxylic acid metabolic process
A0035375molecular_functionzymogen binding
A0046421molecular_functionmethylisocitrate lyase activity
A0046872molecular_functionmetal ion binding
A0071456biological_processcellular response to hypoxia
B0003824molecular_functioncatalytic activity
B0004451molecular_functionisocitrate lyase activity
B0005576cellular_componentextracellular region
B0005829cellular_componentcytosol
B0005886cellular_componentplasma membrane
B0006097biological_processglyoxylate cycle
B0006099biological_processtricarboxylic acid cycle
B0006102biological_processisocitrate metabolic process
B0016829molecular_functionlyase activity
B0019752biological_processcarboxylic acid metabolic process
B0035375molecular_functionzymogen binding
B0046421molecular_functionmethylisocitrate lyase activity
B0046872molecular_functionmetal ion binding
B0071456biological_processcellular response to hypoxia
C0003824molecular_functioncatalytic activity
C0004451molecular_functionisocitrate lyase activity
C0005576cellular_componentextracellular region
C0005829cellular_componentcytosol
C0005886cellular_componentplasma membrane
C0006097biological_processglyoxylate cycle
C0006099biological_processtricarboxylic acid cycle
C0006102biological_processisocitrate metabolic process
C0016829molecular_functionlyase activity
C0019752biological_processcarboxylic acid metabolic process
C0035375molecular_functionzymogen binding
C0046421molecular_functionmethylisocitrate lyase activity
C0046872molecular_functionmetal ion binding
C0071456biological_processcellular response to hypoxia
D0003824molecular_functioncatalytic activity
D0004451molecular_functionisocitrate lyase activity
D0005576cellular_componentextracellular region
D0005829cellular_componentcytosol
D0005886cellular_componentplasma membrane
D0006097biological_processglyoxylate cycle
D0006099biological_processtricarboxylic acid cycle
D0006102biological_processisocitrate metabolic process
D0016829molecular_functionlyase activity
D0019752biological_processcarboxylic acid metabolic process
D0035375molecular_functionzymogen binding
D0046421molecular_functionmethylisocitrate lyase activity
D0046872molecular_functionmetal ion binding
D0071456biological_processcellular response to hypoxia
E0003824molecular_functioncatalytic activity
E0004451molecular_functionisocitrate lyase activity
E0005576cellular_componentextracellular region
E0005829cellular_componentcytosol
E0005886cellular_componentplasma membrane
E0006097biological_processglyoxylate cycle
E0006099biological_processtricarboxylic acid cycle
E0006102biological_processisocitrate metabolic process
E0016829molecular_functionlyase activity
E0019752biological_processcarboxylic acid metabolic process
E0035375molecular_functionzymogen binding
E0046421molecular_functionmethylisocitrate lyase activity
E0046872molecular_functionmetal ion binding
E0071456biological_processcellular response to hypoxia
F0003824molecular_functioncatalytic activity
F0004451molecular_functionisocitrate lyase activity
F0005576cellular_componentextracellular region
F0005829cellular_componentcytosol
F0005886cellular_componentplasma membrane
F0006097biological_processglyoxylate cycle
F0006099biological_processtricarboxylic acid cycle
F0006102biological_processisocitrate metabolic process
F0016829molecular_functionlyase activity
F0019752biological_processcarboxylic acid metabolic process
F0035375molecular_functionzymogen binding
F0046421molecular_functionmethylisocitrate lyase activity
F0046872molecular_functionmetal ion binding
F0071456biological_processcellular response to hypoxia
G0003824molecular_functioncatalytic activity
G0004451molecular_functionisocitrate lyase activity
G0005576cellular_componentextracellular region
G0005829cellular_componentcytosol
G0005886cellular_componentplasma membrane
G0006097biological_processglyoxylate cycle
G0006099biological_processtricarboxylic acid cycle
G0006102biological_processisocitrate metabolic process
G0016829molecular_functionlyase activity
G0019752biological_processcarboxylic acid metabolic process
G0035375molecular_functionzymogen binding
G0046421molecular_functionmethylisocitrate lyase activity
G0046872molecular_functionmetal ion binding
G0071456biological_processcellular response to hypoxia
H0003824molecular_functioncatalytic activity
H0004451molecular_functionisocitrate lyase activity
H0005576cellular_componentextracellular region
H0005829cellular_componentcytosol
H0005886cellular_componentplasma membrane
H0006097biological_processglyoxylate cycle
H0006099biological_processtricarboxylic acid cycle
H0006102biological_processisocitrate metabolic process
H0016829molecular_functionlyase activity
H0019752biological_processcarboxylic acid metabolic process
H0035375molecular_functionzymogen binding
H0046421molecular_functionmethylisocitrate lyase activity
H0046872molecular_functionmetal ion binding
H0071456biological_processcellular response to hypoxia
Functional Information from PDB Data
site_idAC1
Number of Residues14
Detailsbinding site for residue PYR A 501
ChainResidue
ATYR89
ATHR347
AMG502
AHOH611
AHOH620
AHOH650
ASER91
AGLY92
ATRP93
AASP153
AHIS180
AEJA191
AARG228
ATRP283

site_idAC2
Number of Residues5
Detailsbinding site for residue MG A 502
ChainResidue
AASP153
APYR501
AHOH611
AHOH620
AHOH650

site_idAC3
Number of Residues6
Detailsbinding site for residue MG A 503
ChainResidue
AALA276
AALA279
AGLN308
AHOH633
AHOH848
AHOH855

site_idAC4
Number of Residues10
Detailsbinding site for residue 3NP B 502
ChainResidue
ATYR356
ASER357
ALEU376
AARG379
BTYR356
BSER357
BLEU376
BARG379
BHOH601
BHOH648

site_idAC5
Number of Residues14
Detailsbinding site for residue PYR B 503
ChainResidue
BTYR89
BSER91
BGLY92
BTRP93
BASP153
BHIS180
BEJA191
BARG228
BTRP283
BTHR347
BMG504
BHOH606
BHOH612
BHOH661

site_idAC6
Number of Residues5
Detailsbinding site for residue MG B 504
ChainResidue
BASP153
BPYR503
BHOH606
BHOH612
BHOH661

site_idAC7
Number of Residues6
Detailsbinding site for residue MG B 505
ChainResidue
BALA276
BALA279
BGLN308
BHOH734
BHOH811
BHOH826

site_idAC8
Number of Residues2
Detailsbinding site for residue PEG B 506
ChainResidue
BLEU63
BGLU64

site_idAC9
Number of Residues14
Detailsbinding site for residue PYR C 501
ChainResidue
CTYR89
CSER91
CGLY92
CTRP93
CASP153
CHIS180
CEJA191
CARG228
CTRP283
CTHR347
CMG502
CHOH619
CHOH625
CHOH634

site_idAD1
Number of Residues5
Detailsbinding site for residue MG C 502
ChainResidue
CASP153
CPYR501
CHOH619
CHOH625
CHOH634

site_idAD2
Number of Residues6
Detailsbinding site for residue MG C 503
ChainResidue
CALA276
CALA279
CGLN308
CHOH744
CHOH819
CHOH872

site_idAD3
Number of Residues2
Detailsbinding site for residue PEG C 504
ChainResidue
CTRP65
CHOH678

site_idAD4
Number of Residues10
Detailsbinding site for residue 3NP C 505
ChainResidue
CTYR356
CSER357
CARG379
CHOH601
CHOH626
DTYR356
DSER357
DLEU376
DARG379
DHOH646

site_idAD5
Number of Residues14
Detailsbinding site for residue PYR D 501
ChainResidue
DTYR89
DSER91
DGLY92
DTRP93
DASP153
DHIS180
DEJA191
DARG228
DTRP283
DTHR347
DMG502
DHOH605
DHOH612
DHOH653

site_idAD6
Number of Residues5
Detailsbinding site for residue MG D 502
ChainResidue
DASP153
DPYR501
DHOH605
DHOH612
DHOH653

site_idAD7
Number of Residues6
Detailsbinding site for residue MG D 503
ChainResidue
DALA276
DALA279
DGLN308
DHOH771
DHOH836
DHOH849

site_idAD8
Number of Residues3
Detailsbinding site for residue PEG D 504
ChainResidue
CALA366
CGLN369
DTRP65

site_idAD9
Number of Residues14
Detailsbinding site for residue PYR E 501
ChainResidue
ETYR89
ESER91
EGLY92
ETRP93
EASP153
EHIS180
EEJA191
EARG228
ETRP283
ETHR347
EMG502
EHOH608
EHOH636
EHOH664

site_idAE1
Number of Residues5
Detailsbinding site for residue MG E 502
ChainResidue
EASP153
EPYR501
EHOH608
EHOH636
EHOH664

site_idAE2
Number of Residues6
Detailsbinding site for residue MG E 503
ChainResidue
EALA276
EALA279
EGLN308
EHOH662
EHOH920
EHOH928

site_idAE3
Number of Residues3
Detailsbinding site for residue PEG E 504
ChainResidue
ETRP65
FGLN367
FGLN369

site_idAE4
Number of Residues8
Detailsbinding site for residue EPE F 501
ChainResidue
ETYR356
FTYR356
FSER357
FASP360
FARG379
FHOH601
FHOH734
FHOH754

site_idAE5
Number of Residues14
Detailsbinding site for residue PYR F 502
ChainResidue
FTYR89
FSER91
FGLY92
FTRP93
FASP153
FHIS180
FEJA191
FARG228
FTRP283
FTHR347
FMG503
FHOH620
FHOH629
FHOH643

site_idAE6
Number of Residues5
Detailsbinding site for residue MG F 503
ChainResidue
FASP153
FPYR502
FHOH620
FHOH629
FHOH643

site_idAE7
Number of Residues6
Detailsbinding site for residue MG F 504
ChainResidue
FHOH624
FHOH667
FHOH829
FHOH933
GHOH808
GHOH893

site_idAE8
Number of Residues6
Detailsbinding site for residue MG F 505
ChainResidue
FALA276
FALA279
FGLN308
FHOH692
FHOH910
FHOH914

site_idAE9
Number of Residues3
Detailsbinding site for residue PEG F 506
ChainResidue
FLEU63
FTRP65
FASN67

site_idAF1
Number of Residues14
Detailsbinding site for residue PYR G 501
ChainResidue
GTYR89
GSER91
GGLY92
GTRP93
GASP153
GHIS180
GEJA191
GARG228
GTRP283
GTHR347
GMG502
GHOH603
GHOH629
GHOH680

site_idAF2
Number of Residues5
Detailsbinding site for residue MG G 502
ChainResidue
GASP153
GPYR501
GHOH603
GHOH629
GHOH680

site_idAF3
Number of Residues7
Detailsbinding site for residue EPE G 503
ChainResidue
GSER357
GARG379
GHOH662
HTYR356
HSER357
HARG379
HHOH746

site_idAF4
Number of Residues6
Detailsbinding site for residue MG G 504
ChainResidue
GALA276
GALA279
GGLN308
GHOH606
GHOH895
GHOH906

site_idAF5
Number of Residues3
Detailsbinding site for residue PEG G 505
ChainResidue
GGLU64
GTRP65
GLYS334

site_idAF6
Number of Residues5
Detailsbinding site for residue MG G 506
ChainResidue
EHOH907
GHOH739
HHOH643
HHOH895
HHOH911

site_idAF7
Number of Residues5
Detailsbinding site for residue MG H 501
ChainResidue
EHOH910
HASP34
HHOH624
HHOH736
HHOH762

site_idAF8
Number of Residues14
Detailsbinding site for residue PYR H 502
ChainResidue
HTYR89
HSER91
HGLY92
HTRP93
HASP153
HHIS180
HEJA191
HARG228
HTRP283
HTHR347
HMG503
HHOH605
HHOH648
HHOH652

site_idAF9
Number of Residues5
Detailsbinding site for residue MG H 503
ChainResidue
HASP153
HPYR502
HHOH605
HHOH648
HHOH652

site_idAG1
Number of Residues6
Detailsbinding site for residue MG H 504
ChainResidue
FHOH965
GHOH953
HHOH640
HHOH696
HHOH698
HHOH856

site_idAG2
Number of Residues6
Detailsbinding site for residue MG H 505
ChainResidue
HALA276
HALA279
HGLN308
HHOH645
HHOH877
HHOH896

site_idAG3
Number of Residues4
Detailsbinding site for residue PEG H 506
ChainResidue
HTRP65
HASN67
HHOH777
HHOH843

Functional Information from SwissProt/UniProt
site_idSWS_FT_FI1
Number of Residues8
DetailsActive site: {"description":"Proton acceptor","evidences":[{"source":"PubMed","id":"24354272","evidenceCode":"ECO:0000305"}]}
ChainResidueDetails

site_idSWS_FT_FI2
Number of Residues80
DetailsBinding site: {"evidences":[{"source":"PubMed","id":"10932251","evidenceCode":"ECO:0000269"}]}
ChainResidueDetails

site_idSWS_FT_FI3
Number of Residues16
DetailsCross-link: {"description":"Isoglutamyl lysine isopeptide (Lys-Gln) (interchain with Q-Cter in protein Pup)","evidences":[{"source":"PubMed","id":"20066036","evidenceCode":"ECO:0000269"}]}
ChainResidueDetails

Catalytic Information from CSA
site_idMCSA1
Number of Residues7
DetailsM-CSA 272
ChainResidueDetails
AASP153metal ligand
AHIS180electrostatic stabiliser, hydrogen bond donor
AEJA191covalent catalysis, hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor, proton relay, proton shuttle (general acid/base)
ALYS197hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor, proton shuttle (general acid/base)
AGLU232electrostatic stabiliser, hydrogen bond donor
AASN319electrostatic stabiliser, hydrogen bond donor
ALYS321electrostatic stabiliser, hydrogen bond donor

site_idMCSA2
Number of Residues7
DetailsM-CSA 272
ChainResidueDetails
BASP153metal ligand
BHIS180electrostatic stabiliser, hydrogen bond donor
BEJA191covalent catalysis, hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor, proton relay, proton shuttle (general acid/base)
BLYS197hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor, proton shuttle (general acid/base)
BGLU232electrostatic stabiliser, hydrogen bond donor
BASN319electrostatic stabiliser, hydrogen bond donor
BLYS321electrostatic stabiliser, hydrogen bond donor

site_idMCSA3
Number of Residues7
DetailsM-CSA 272
ChainResidueDetails
CASP153metal ligand
CHIS180electrostatic stabiliser, hydrogen bond donor
CEJA191covalent catalysis, hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor, proton relay, proton shuttle (general acid/base)
CLYS197hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor, proton shuttle (general acid/base)
CGLU232electrostatic stabiliser, hydrogen bond donor
CASN319electrostatic stabiliser, hydrogen bond donor
CLYS321electrostatic stabiliser, hydrogen bond donor

site_idMCSA4
Number of Residues7
DetailsM-CSA 272
ChainResidueDetails
DASP153metal ligand
DHIS180electrostatic stabiliser, hydrogen bond donor
DEJA191covalent catalysis, hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor, proton relay, proton shuttle (general acid/base)
DLYS197hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor, proton shuttle (general acid/base)
DGLU232electrostatic stabiliser, hydrogen bond donor
DASN319electrostatic stabiliser, hydrogen bond donor
DLYS321electrostatic stabiliser, hydrogen bond donor

site_idMCSA5
Number of Residues7
DetailsM-CSA 272
ChainResidueDetails
EASP153metal ligand
EHIS180electrostatic stabiliser, hydrogen bond donor
EEJA191covalent catalysis, hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor, proton relay, proton shuttle (general acid/base)
ELYS197hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor, proton shuttle (general acid/base)
EGLU232electrostatic stabiliser, hydrogen bond donor
EASN319electrostatic stabiliser, hydrogen bond donor
ELYS321electrostatic stabiliser, hydrogen bond donor

site_idMCSA6
Number of Residues7
DetailsM-CSA 272
ChainResidueDetails
FASP153metal ligand
FHIS180electrostatic stabiliser, hydrogen bond donor
FEJA191covalent catalysis, hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor, proton relay, proton shuttle (general acid/base)
FLYS197hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor, proton shuttle (general acid/base)
FGLU232electrostatic stabiliser, hydrogen bond donor
FASN319electrostatic stabiliser, hydrogen bond donor
FLYS321electrostatic stabiliser, hydrogen bond donor

site_idMCSA7
Number of Residues7
DetailsM-CSA 272
ChainResidueDetails
GASP153metal ligand
GHIS180electrostatic stabiliser, hydrogen bond donor
GEJA191covalent catalysis, hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor, proton relay, proton shuttle (general acid/base)
GLYS197hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor, proton shuttle (general acid/base)
GGLU232electrostatic stabiliser, hydrogen bond donor
GASN319electrostatic stabiliser, hydrogen bond donor
GLYS321electrostatic stabiliser, hydrogen bond donor

site_idMCSA8
Number of Residues7
DetailsM-CSA 272
ChainResidueDetails
HASP153metal ligand
HHIS180electrostatic stabiliser, hydrogen bond donor
HEJA191covalent catalysis, hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor, proton relay, proton shuttle (general acid/base)
HLYS197hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor, proton shuttle (general acid/base)
HGLU232electrostatic stabiliser, hydrogen bond donor
HASN319electrostatic stabiliser, hydrogen bond donor
HLYS321electrostatic stabiliser, hydrogen bond donor

243083

PDB entries from 2025-10-15

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