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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
A0052572biological_processresponse to host immune response
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
B0052572biological_processresponse to host immune response
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
C0052572biological_processresponse to host immune response
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
D0052572biological_processresponse to host immune response
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
E0052572biological_processresponse to host immune response
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
F0052572biological_processresponse to host immune response
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
G0052572biological_processresponse to host immune response
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
H0052572biological_processresponse to host immune response
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
DetailsACT_SITE: Proton acceptor => ECO:0000305|PubMed:24354272
ChainResidueDetails
AEJA191
BEJA191
CEJA191
DEJA191
EEJA191
FEJA191
GEJA191
HEJA191

site_idSWS_FT_FI2
Number of Residues48
DetailsBINDING: BINDING => ECO:0000269|PubMed:10932251
ChainResidueDetails
ASER91
BARG228
BASN313
BTHR347
CSER91
CASP153
CGLY192
CARG228
CASN313
CTHR347
DSER91
AASP153
DASP153
DGLY192
DARG228
DASN313
DTHR347
ESER91
EASP153
EGLY192
EARG228
EASN313
AGLY192
ETHR347
FSER91
FASP153
FGLY192
FARG228
FASN313
FTHR347
GSER91
GASP153
GGLY192
AARG228
GARG228
GASN313
GTHR347
HSER91
HASP153
HGLY192
HARG228
HASN313
HTHR347
AASN313
ATHR347
BSER91
BASP153
BGLY192

site_idSWS_FT_FI3
Number of Residues16
DetailsCROSSLNK: Isoglutamyl lysine isopeptide (Lys-Gln) (interchain with Q-Cter in protein Pup) => ECO:0000269|PubMed:20066036
ChainResidueDetails
ALYS334
FLYS334
GLYS334
HLYS334
BLYS334
CLYS334
DLYS334
ELYS334

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)
AHIS193hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor, proton shuttle (general acid/base)
AARG228electrostatic stabiliser, hydrogen bond donor
ASER315electrostatic stabiliser, hydrogen bond donor
ASER317electrostatic 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)
BHIS193hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor, proton shuttle (general acid/base)
BARG228electrostatic stabiliser, hydrogen bond donor
BSER315electrostatic stabiliser, hydrogen bond donor
BSER317electrostatic 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)
CHIS193hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor, proton shuttle (general acid/base)
CARG228electrostatic stabiliser, hydrogen bond donor
CSER315electrostatic stabiliser, hydrogen bond donor
CSER317electrostatic 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)
DHIS193hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor, proton shuttle (general acid/base)
DARG228electrostatic stabiliser, hydrogen bond donor
DSER315electrostatic stabiliser, hydrogen bond donor
DSER317electrostatic 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)
EHIS193hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor, proton shuttle (general acid/base)
EARG228electrostatic stabiliser, hydrogen bond donor
ESER315electrostatic stabiliser, hydrogen bond donor
ESER317electrostatic 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)
FHIS193hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor, proton shuttle (general acid/base)
FARG228electrostatic stabiliser, hydrogen bond donor
FSER315electrostatic stabiliser, hydrogen bond donor
FSER317electrostatic 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)
GHIS193hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor, proton shuttle (general acid/base)
GARG228electrostatic stabiliser, hydrogen bond donor
GSER315electrostatic stabiliser, hydrogen bond donor
GSER317electrostatic 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)
HHIS193hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor, proton shuttle (general acid/base)
HARG228electrostatic stabiliser, hydrogen bond donor
HSER315electrostatic stabiliser, hydrogen bond donor
HSER317electrostatic stabiliser, hydrogen bond donor

224931

PDB entries from 2024-09-11

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