6VB9
Covalent adduct of cis-2,3-epoxysuccinic acid with Isocitrate Lyase-1 from Mycobacterium tuberculosis
Functional Information from GO Data
Chain | GOid | namespace | contents |
A | 0003824 | molecular_function | catalytic activity |
A | 0004451 | molecular_function | isocitrate lyase activity |
A | 0005576 | cellular_component | extracellular region |
A | 0005829 | cellular_component | cytosol |
A | 0005886 | cellular_component | plasma membrane |
A | 0006097 | biological_process | glyoxylate cycle |
A | 0006099 | biological_process | tricarboxylic acid cycle |
A | 0006102 | biological_process | isocitrate metabolic process |
A | 0016829 | molecular_function | lyase activity |
A | 0019752 | biological_process | carboxylic acid metabolic process |
A | 0035375 | molecular_function | zymogen binding |
A | 0046421 | molecular_function | methylisocitrate lyase activity |
A | 0046872 | molecular_function | metal ion binding |
A | 0052572 | biological_process | response to host immune response |
A | 0071456 | biological_process | cellular response to hypoxia |
B | 0003824 | molecular_function | catalytic activity |
B | 0004451 | molecular_function | isocitrate lyase activity |
B | 0005576 | cellular_component | extracellular region |
B | 0005829 | cellular_component | cytosol |
B | 0005886 | cellular_component | plasma membrane |
B | 0006097 | biological_process | glyoxylate cycle |
B | 0006099 | biological_process | tricarboxylic acid cycle |
B | 0006102 | biological_process | isocitrate metabolic process |
B | 0016829 | molecular_function | lyase activity |
B | 0019752 | biological_process | carboxylic acid metabolic process |
B | 0035375 | molecular_function | zymogen binding |
B | 0046421 | molecular_function | methylisocitrate lyase activity |
B | 0046872 | molecular_function | metal ion binding |
B | 0052572 | biological_process | response to host immune response |
B | 0071456 | biological_process | cellular response to hypoxia |
C | 0003824 | molecular_function | catalytic activity |
C | 0004451 | molecular_function | isocitrate lyase activity |
C | 0005576 | cellular_component | extracellular region |
C | 0005829 | cellular_component | cytosol |
C | 0005886 | cellular_component | plasma membrane |
C | 0006097 | biological_process | glyoxylate cycle |
C | 0006099 | biological_process | tricarboxylic acid cycle |
C | 0006102 | biological_process | isocitrate metabolic process |
C | 0016829 | molecular_function | lyase activity |
C | 0019752 | biological_process | carboxylic acid metabolic process |
C | 0035375 | molecular_function | zymogen binding |
C | 0046421 | molecular_function | methylisocitrate lyase activity |
C | 0046872 | molecular_function | metal ion binding |
C | 0052572 | biological_process | response to host immune response |
C | 0071456 | biological_process | cellular response to hypoxia |
D | 0003824 | molecular_function | catalytic activity |
D | 0004451 | molecular_function | isocitrate lyase activity |
D | 0005576 | cellular_component | extracellular region |
D | 0005829 | cellular_component | cytosol |
D | 0005886 | cellular_component | plasma membrane |
D | 0006097 | biological_process | glyoxylate cycle |
D | 0006099 | biological_process | tricarboxylic acid cycle |
D | 0006102 | biological_process | isocitrate metabolic process |
D | 0016829 | molecular_function | lyase activity |
D | 0019752 | biological_process | carboxylic acid metabolic process |
D | 0035375 | molecular_function | zymogen binding |
D | 0046421 | molecular_function | methylisocitrate lyase activity |
D | 0046872 | molecular_function | metal ion binding |
D | 0052572 | biological_process | response to host immune response |
D | 0071456 | biological_process | cellular response to hypoxia |
Functional Information from PDB Data
site_id | AC1 |
Number of Residues | 5 |
Details | binding site for residue MG A 501 |
Chain | Residue |
A | ASP153 |
A | OXD503 |
A | HOH606 |
A | HOH622 |
A | HOH643 |
site_id | AC2 |
Number of Residues | 6 |
Details | binding site for residue MG A 502 |
Chain | Residue |
A | HOH818 |
A | HOH827 |
A | ALA276 |
A | ALA279 |
A | GLN308 |
A | HOH765 |
site_id | AC3 |
Number of Residues | 14 |
Details | binding site for residue OXD A 503 |
Chain | Residue |
A | TYR89 |
A | SER91 |
A | GLY92 |
A | TRP93 |
A | ASP153 |
A | HIS180 |
A | QVA191 |
A | ARG228 |
A | TRP283 |
A | THR347 |
A | MG501 |
A | HOH606 |
A | HOH622 |
A | HOH643 |
site_id | AC4 |
Number of Residues | 3 |
Details | binding site for residue ACY A 504 |
Chain | Residue |
A | TRP65 |
A | HOH624 |
B | HOH654 |
site_id | AC5 |
Number of Residues | 3 |
Details | binding site for residue ACY A 505 |
Chain | Residue |
A | PRO21 |
A | TRP57 |
A | GLU58 |
site_id | AC6 |
Number of Residues | 5 |
Details | binding site for residue MG B 501 |
Chain | Residue |
B | ASP153 |
B | OXD503 |
B | HOH602 |
B | HOH619 |
B | HOH645 |
site_id | AC7 |
Number of Residues | 6 |
Details | binding site for residue PEG B 502 |
Chain | Residue |
B | LEU185 |
B | GLN204 |
B | THR238 |
B | HOH813 |
C | LEU185 |
C | SER187 |
site_id | AC8 |
Number of Residues | 13 |
Details | binding site for residue OXD B 503 |
Chain | Residue |
B | TYR89 |
B | SER91 |
B | GLY92 |
B | TRP93 |
B | ASP153 |
B | HIS180 |
B | QVA191 |
B | ARG228 |
B | TRP283 |
B | THR347 |
B | MG501 |
B | HOH602 |
B | HOH645 |
site_id | AC9 |
Number of Residues | 4 |
Details | binding site for residue ACY B 504 |
Chain | Residue |
B | TRP17 |
B | TRP23 |
B | ARG28 |
B | ASP217 |
site_id | AD1 |
Number of Residues | 3 |
Details | binding site for residue ACY B 505 |
Chain | Residue |
B | GLN204 |
B | ARG207 |
D | ASP410 |
site_id | AD2 |
Number of Residues | 1 |
Details | binding site for residue ACY B 506 |
Chain | Residue |
B | TRP65 |
site_id | AD3 |
Number of Residues | 5 |
Details | binding site for residue MG C 501 |
Chain | Residue |
C | ASP153 |
C | OXD504 |
C | HOH614 |
C | HOH628 |
C | HOH640 |
site_id | AD4 |
Number of Residues | 6 |
Details | binding site for residue MG C 502 |
Chain | Residue |
C | ALA276 |
C | ALA279 |
C | GLN308 |
C | HOH636 |
C | HOH800 |
C | HOH814 |
site_id | AD5 |
Number of Residues | 12 |
Details | binding site for residue PEG C 503 |
Chain | Residue |
C | VAL78 |
C | GLN79 |
C | ARG82 |
C | ALA131 |
C | ILE134 |
C | ALA135 |
C | TRP146 |
C | THR389 |
C | ARG395 |
C | GLU396 |
C | HOH607 |
C | HOH647 |
site_id | AD6 |
Number of Residues | 14 |
Details | binding site for residue OXD C 504 |
Chain | Residue |
C | HOH640 |
C | TYR89 |
C | SER91 |
C | GLY92 |
C | TRP93 |
C | ASP153 |
C | HIS180 |
C | QVA191 |
C | ARG228 |
C | TRP283 |
C | THR347 |
C | MG501 |
C | HOH614 |
C | HOH628 |
site_id | AD7 |
Number of Residues | 2 |
Details | binding site for residue ACY C 505 |
Chain | Residue |
C | TRP65 |
C | ASN67 |
site_id | AD8 |
Number of Residues | 6 |
Details | binding site for residue MG D 501 |
Chain | Residue |
D | ALA276 |
D | ALA279 |
D | GLN308 |
D | HOH730 |
D | HOH738 |
D | HOH796 |
site_id | AD9 |
Number of Residues | 5 |
Details | binding site for residue MG D 502 |
Chain | Residue |
D | ASP153 |
D | OXD503 |
D | HOH605 |
D | HOH620 |
D | HOH633 |
site_id | AE1 |
Number of Residues | 12 |
Details | binding site for residue OXD D 503 |
Chain | Residue |
D | TYR89 |
D | SER91 |
D | GLY92 |
D | TRP93 |
D | ASP153 |
D | HIS180 |
D | QVA191 |
D | ARG228 |
D | THR347 |
D | MG502 |
D | HOH620 |
D | HOH633 |
site_id | AE2 |
Number of Residues | 5 |
Details | binding site for residue ACY D 504 |
Chain | Residue |
D | TRP17 |
D | TRP23 |
D | ASP217 |
D | ASP220 |
D | VAL221 |
site_id | AE3 |
Number of Residues | 5 |
Details | binding site for residue ACY D 505 |
Chain | Residue |
D | PRO7 |
D | LYS8 |
D | ILE13 |
D | GLN39 |
D | ASP220 |
site_id | AE4 |
Number of Residues | 2 |
Details | binding site for residue ACY D 506 |
Chain | Residue |
D | GLU64 |
D | TRP65 |
Functional Information from PROSITE/UniProt
site_id | PS00161 |
Number of Residues | 6 |
Details | ISOCITRATE_LYASE Isocitrate lyase signature. KKCGHL |
Chain | Residue | Details |
A | LYS189-LEU194 |
Functional Information from SwissProt/UniProt
site_id | SWS_FT_FI1 |
Number of Residues | 4 |
Details | ACT_SITE: Proton acceptor => ECO:0000305|PubMed:24354272 |
Chain | Residue | Details |
A | QVA191 | |
B | QVA191 | |
C | QVA191 | |
D | QVA191 |
site_id | SWS_FT_FI2 |
Number of Residues | 24 |
Details | BINDING: BINDING => ECO:0000269|PubMed:10932251 |
Chain | Residue | Details |
A | SER91 | |
B | ARG228 | |
B | ASN313 | |
B | THR347 | |
C | SER91 | |
C | ASP153 | |
C | GLY192 | |
C | ARG228 | |
C | ASN313 | |
C | THR347 | |
D | SER91 | |
A | ASP153 | |
D | ASP153 | |
D | GLY192 | |
D | ARG228 | |
D | ASN313 | |
D | THR347 | |
A | GLY192 | |
A | ARG228 | |
A | ASN313 | |
A | THR347 | |
B | SER91 | |
B | ASP153 | |
B | GLY192 |
site_id | SWS_FT_FI3 |
Number of Residues | 8 |
Details | CROSSLNK: Isoglutamyl lysine isopeptide (Lys-Gln) (interchain with Q-Cter in protein Pup) => ECO:0000269|PubMed:20066036 |
Chain | Residue | Details |
A | LYS334 | |
B | LYS334 | |
C | LYS334 | |
D | LYS334 |
Catalytic Information from CSA
site_id | MCSA1 |
Number of Residues | 7 |
Details | M-CSA 272 |
Chain | Residue | Details |
A | ASP153 | metal ligand |
A | HIS180 | electrostatic stabiliser, hydrogen bond donor |
A | QVA191 | covalent catalysis, hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor, proton relay, proton shuttle (general acid/base) |
A | HIS193 | hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor, proton shuttle (general acid/base) |
A | ARG228 | electrostatic stabiliser, hydrogen bond donor |
A | SER315 | electrostatic stabiliser, hydrogen bond donor |
A | SER317 | electrostatic stabiliser, hydrogen bond donor |
site_id | MCSA2 |
Number of Residues | 7 |
Details | M-CSA 272 |
Chain | Residue | Details |
B | ASP153 | metal ligand |
B | HIS180 | electrostatic stabiliser, hydrogen bond donor |
B | QVA191 | covalent catalysis, hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor, proton relay, proton shuttle (general acid/base) |
B | HIS193 | hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor, proton shuttle (general acid/base) |
B | ARG228 | electrostatic stabiliser, hydrogen bond donor |
B | SER315 | electrostatic stabiliser, hydrogen bond donor |
B | SER317 | electrostatic stabiliser, hydrogen bond donor |
site_id | MCSA3 |
Number of Residues | 7 |
Details | M-CSA 272 |
Chain | Residue | Details |
C | ASP153 | metal ligand |
C | HIS180 | electrostatic stabiliser, hydrogen bond donor |
C | QVA191 | covalent catalysis, hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor, proton relay, proton shuttle (general acid/base) |
C | HIS193 | hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor, proton shuttle (general acid/base) |
C | ARG228 | electrostatic stabiliser, hydrogen bond donor |
C | SER315 | electrostatic stabiliser, hydrogen bond donor |
C | SER317 | electrostatic stabiliser, hydrogen bond donor |
site_id | MCSA4 |
Number of Residues | 7 |
Details | M-CSA 272 |
Chain | Residue | Details |
D | ASP153 | metal ligand |
D | HIS180 | electrostatic stabiliser, hydrogen bond donor |
D | QVA191 | covalent catalysis, hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor, proton relay, proton shuttle (general acid/base) |
D | HIS193 | hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor, proton shuttle (general acid/base) |
D | ARG228 | electrostatic stabiliser, hydrogen bond donor |
D | SER315 | electrostatic stabiliser, hydrogen bond donor |
D | SER317 | electrostatic stabiliser, hydrogen bond donor |