6WSI
Intact cis-2,3-epoxysuccinic acid bound to 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 | GLV503 |
A | HOH613 |
A | HOH616 |
A | HOH663 |
site_id | AC2 |
Number of Residues | 6 |
Details | binding site for residue MG A 502 |
Chain | Residue |
A | HOH706 |
A | HOH850 |
A | ALA276 |
A | ALA279 |
A | GLN308 |
A | GOL505 |
site_id | AC3 |
Number of Residues | 12 |
Details | binding site for residue GLV A 503 |
Chain | Residue |
A | TYR89 |
A | SER91 |
A | GLY92 |
A | TRP93 |
A | ASP153 |
A | ARG228 |
A | THR347 |
A | MG501 |
A | U9S504 |
A | HOH613 |
A | HOH616 |
A | HOH663 |
site_id | AC4 |
Number of Residues | 11 |
Details | binding site for residue U9S A 504 |
Chain | Residue |
A | CYS191 |
A | GLY192 |
A | HIS193 |
A | ARG228 |
A | GLU285 |
A | ASN313 |
A | SER315 |
A | SER317 |
A | THR347 |
A | GLV503 |
A | HOH613 |
site_id | AC5 |
Number of Residues | 9 |
Details | binding site for residue GOL A 505 |
Chain | Residue |
A | ALA279 |
A | ASP280 |
A | ASP307 |
A | GLN308 |
A | MET309 |
A | MG502 |
A | HOH607 |
A | HOH608 |
A | HOH639 |
site_id | AC6 |
Number of Residues | 7 |
Details | binding site for residue GOL A 506 |
Chain | Residue |
A | GLU16 |
A | TRP17 |
A | ASP217 |
A | VAL221 |
A | PRO222 |
A | HOH738 |
A | HOH780 |
site_id | AC7 |
Number of Residues | 9 |
Details | binding site for residue PEG A 507 |
Chain | Residue |
A | ALA399 |
A | PHE402 |
A | ASP403 |
A | ALA406 |
A | THR415 |
A | THR416 |
A | HOH601 |
B | GLN109 |
C | LEU162 |
site_id | AC8 |
Number of Residues | 5 |
Details | binding site for residue MG B 501 |
Chain | Residue |
B | ASP153 |
B | GLV503 |
B | HOH612 |
B | HOH619 |
B | HOH629 |
site_id | AC9 |
Number of Residues | 6 |
Details | binding site for residue MG B 502 |
Chain | Residue |
B | ALA276 |
B | ALA279 |
B | GLN308 |
B | GOL506 |
B | HOH706 |
B | HOH842 |
site_id | AD1 |
Number of Residues | 11 |
Details | binding site for residue GLV B 503 |
Chain | Residue |
B | TYR89 |
B | SER91 |
B | GLY92 |
B | TRP93 |
B | ASP153 |
B | ARG228 |
B | THR347 |
B | MG501 |
B | U9S504 |
B | HOH619 |
B | HOH629 |
site_id | AD2 |
Number of Residues | 12 |
Details | binding site for residue U9S B 504 |
Chain | Residue |
B | TRP93 |
B | CYS191 |
B | GLY192 |
B | HIS193 |
B | ARG228 |
B | GLU285 |
B | ASN313 |
B | SER315 |
B | SER317 |
B | THR347 |
B | GLV503 |
B | HOH619 |
site_id | AD3 |
Number of Residues | 7 |
Details | binding site for residue GOL B 505 |
Chain | Residue |
B | LEU236 |
A | THR419 |
B | GLY195 |
B | GLY196 |
B | LYS197 |
B | ALA234 |
B | THR235 |
site_id | AD4 |
Number of Residues | 9 |
Details | binding site for residue GOL B 506 |
Chain | Residue |
B | ALA279 |
B | ASP280 |
B | ASP307 |
B | GLN308 |
B | MET309 |
B | MG502 |
B | HOH603 |
B | HOH671 |
B | HOH772 |
site_id | AD5 |
Number of Residues | 11 |
Details | binding site for residue GOL B 507 |
Chain | Residue |
A | ARG123 |
B | ASP98 |
B | ALA99 |
B | ASN100 |
B | GLY103 |
B | HOH614 |
B | HOH617 |
B | HOH757 |
B | HOH759 |
B | HOH791 |
B | HOH839 |
site_id | AD6 |
Number of Residues | 7 |
Details | binding site for residue GOL B 508 |
Chain | Residue |
B | GLU16 |
B | TRP17 |
B | ASP217 |
B | VAL221 |
B | PRO222 |
B | HOH703 |
B | HOH735 |
site_id | AD7 |
Number of Residues | 8 |
Details | binding site for residue GOL B 509 |
Chain | Residue |
B | VAL78 |
B | ARG82 |
B | ALA131 |
B | TRP146 |
B | THR389 |
B | ARG395 |
B | GLU396 |
B | HOH691 |
site_id | AD8 |
Number of Residues | 9 |
Details | binding site for residue PEG B 510 |
Chain | Residue |
B | LEU199 |
B | ARG244 |
B | ASP245 |
B | PHE248 |
B | PRO267 |
B | ARG271 |
B | HOH645 |
B | HOH670 |
B | HOH701 |
site_id | AD9 |
Number of Residues | 5 |
Details | binding site for residue MG C 501 |
Chain | Residue |
C | ASP153 |
C | GLV503 |
C | HOH611 |
C | HOH612 |
C | HOH655 |
site_id | AE1 |
Number of Residues | 6 |
Details | binding site for residue MG C 502 |
Chain | Residue |
C | ALA276 |
C | ALA279 |
C | GLN308 |
C | GOL505 |
C | HOH710 |
C | HOH858 |
site_id | AE2 |
Number of Residues | 13 |
Details | binding site for residue GLV C 503 |
Chain | Residue |
C | TYR89 |
C | SER91 |
C | GLY92 |
C | TRP93 |
C | ASP153 |
C | HIS180 |
C | ARG228 |
C | THR347 |
C | MG501 |
C | U9S504 |
C | HOH611 |
C | HOH612 |
C | HOH655 |
site_id | AE3 |
Number of Residues | 12 |
Details | binding site for residue U9S C 504 |
Chain | Residue |
C | TRP93 |
C | CYS191 |
C | GLY192 |
C | HIS193 |
C | ARG228 |
C | GLU285 |
C | ASN313 |
C | SER315 |
C | SER317 |
C | THR347 |
C | GLV503 |
C | HOH612 |
site_id | AE4 |
Number of Residues | 9 |
Details | binding site for residue GOL C 505 |
Chain | Residue |
C | ALA279 |
C | ASP280 |
C | ASP307 |
C | GLN308 |
C | MET309 |
C | MG502 |
C | HOH603 |
C | HOH675 |
C | HOH764 |
site_id | AE5 |
Number of Residues | 7 |
Details | binding site for residue GOL C 506 |
Chain | Residue |
C | GLU16 |
C | TRP17 |
C | ASP217 |
C | VAL221 |
C | PRO222 |
C | HOH626 |
C | HOH648 |
site_id | AE6 |
Number of Residues | 7 |
Details | binding site for residue GOL C 507 |
Chain | Residue |
C | GLY195 |
C | GLY196 |
C | LYS197 |
C | ALA233 |
C | THR235 |
C | LEU236 |
C | HOH632 |
site_id | AE7 |
Number of Residues | 6 |
Details | binding site for residue PEG C 508 |
Chain | Residue |
A | THR407 |
A | THR408 |
C | THR29 |
C | ASP34 |
C | HOH618 |
C | HOH627 |
site_id | AE8 |
Number of Residues | 6 |
Details | binding site for residue MG D 501 |
Chain | Residue |
D | ALA276 |
D | ALA279 |
D | GLN308 |
D | GOL505 |
D | HOH673 |
D | HOH846 |
site_id | AE9 |
Number of Residues | 5 |
Details | binding site for residue MG D 502 |
Chain | Residue |
D | ASP153 |
D | GLV503 |
D | HOH612 |
D | HOH623 |
D | HOH677 |
site_id | AF1 |
Number of Residues | 12 |
Details | binding site for residue GLV D 503 |
Chain | Residue |
D | TYR89 |
D | SER91 |
D | GLY92 |
D | TRP93 |
D | ASP153 |
D | HIS180 |
D | ARG228 |
D | THR347 |
D | MG502 |
D | U9S504 |
D | HOH623 |
D | HOH677 |
site_id | AF2 |
Number of Residues | 12 |
Details | binding site for residue U9S D 504 |
Chain | Residue |
D | TRP93 |
D | CYS191 |
D | GLY192 |
D | HIS193 |
D | ARG228 |
D | GLU285 |
D | ASN313 |
D | SER315 |
D | SER317 |
D | THR347 |
D | GLV503 |
D | HOH623 |
site_id | AF3 |
Number of Residues | 8 |
Details | binding site for residue GOL D 505 |
Chain | Residue |
D | ALA279 |
D | ASP280 |
D | ASP307 |
D | GLN308 |
D | MET309 |
D | MG501 |
D | HOH634 |
D | HOH658 |
site_id | AF4 |
Number of Residues | 6 |
Details | binding site for residue GOL D 506 |
Chain | Residue |
D | GLY195 |
D | GLY196 |
D | LYS197 |
D | ALA233 |
D | THR235 |
D | HOH643 |
site_id | AF5 |
Number of Residues | 8 |
Details | binding site for residue GOL D 507 |
Chain | Residue |
D | GLU16 |
D | TRP17 |
D | ASP217 |
D | VAL221 |
D | PRO222 |
D | PEG508 |
D | HOH631 |
D | HOH720 |
site_id | AF6 |
Number of Residues | 7 |
Details | binding site for residue PEG D 508 |
Chain | Residue |
D | GLU16 |
D | ASN20 |
D | TRP23 |
D | PRO222 |
D | GOL507 |
D | HOH613 |
D | HOH675 |
site_id | AF7 |
Number of Residues | 9 |
Details | binding site for residue PEG D 509 |
Chain | Residue |
B | LEU162 |
C | GLN109 |
D | ALA399 |
D | PHE402 |
D | ASP403 |
D | ALA406 |
D | THR415 |
D | HOH606 |
D | HOH609 |
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 | CYS191 | |
B | CYS191 | |
C | CYS191 | |
D | CYS191 |
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 | CYS191 | 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 | CYS191 | 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 | CYS191 | 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 | CYS191 | 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 |