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 | 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 | 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 | 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 | 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 | Active site: {"description":"Proton acceptor","evidences":[{"source":"PubMed","id":"24354272","evidenceCode":"ECO:0000305"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI2 |
| Number of Residues | 40 |
| Details | Binding site: {"evidences":[{"source":"PubMed","id":"10932251","evidenceCode":"ECO:0000269"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI3 |
| Number of Residues | 8 |
| Details | Cross-link: {"description":"Isoglutamyl lysine isopeptide (Lys-Gln) (interchain with Q-Cter in protein Pup)","evidences":[{"source":"PubMed","id":"20066036","evidenceCode":"ECO:0000269"}]} |
| Chain | Residue | Details |
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 |
