6NUB
Pyruvate Kinase M2 Mutant - S437Y in Complex with L-serine
Functional Information from GO Data
| Chain | GOid | namespace | contents |
| A | 0000287 | molecular_function | magnesium ion binding |
| A | 0003723 | molecular_function | RNA binding |
| A | 0003729 | molecular_function | mRNA binding |
| A | 0003824 | molecular_function | catalytic activity |
| A | 0004713 | molecular_function | protein tyrosine kinase activity |
| A | 0004743 | molecular_function | pyruvate kinase activity |
| A | 0005515 | molecular_function | protein binding |
| A | 0005524 | molecular_function | ATP binding |
| A | 0005576 | cellular_component | extracellular region |
| A | 0005634 | cellular_component | nucleus |
| A | 0005737 | cellular_component | cytoplasm |
| A | 0005739 | cellular_component | mitochondrion |
| A | 0005791 | cellular_component | rough endoplasmic reticulum |
| A | 0005829 | cellular_component | cytosol |
| A | 0005929 | cellular_component | cilium |
| A | 0006096 | biological_process | glycolytic process |
| A | 0006417 | biological_process | regulation of translation |
| A | 0012501 | biological_process | programmed cell death |
| A | 0016301 | molecular_function | kinase activity |
| A | 0023026 | molecular_function | MHC class II protein complex binding |
| A | 0030955 | molecular_function | potassium ion binding |
| A | 0031982 | cellular_component | vesicle |
| A | 0032869 | biological_process | cellular response to insulin stimulus |
| A | 0034774 | cellular_component | secretory granule lumen |
| A | 0045296 | molecular_function | cadherin binding |
| A | 0046872 | molecular_function | metal ion binding |
| A | 0061621 | biological_process | canonical glycolysis |
| A | 0062023 | cellular_component | collagen-containing extracellular matrix |
| A | 0070062 | cellular_component | extracellular exosome |
| A | 1903561 | cellular_component | extracellular vesicle |
| A | 1903672 | biological_process | positive regulation of sprouting angiogenesis |
| A | 1904813 | cellular_component | ficolin-1-rich granule lumen |
| A | 2000767 | biological_process | positive regulation of cytoplasmic translation |
| B | 0000287 | molecular_function | magnesium ion binding |
| B | 0003723 | molecular_function | RNA binding |
| B | 0003729 | molecular_function | mRNA binding |
| B | 0003824 | molecular_function | catalytic activity |
| B | 0004713 | molecular_function | protein tyrosine kinase activity |
| B | 0004743 | molecular_function | pyruvate kinase activity |
| B | 0005515 | molecular_function | protein binding |
| B | 0005524 | molecular_function | ATP binding |
| B | 0005576 | cellular_component | extracellular region |
| B | 0005634 | cellular_component | nucleus |
| B | 0005737 | cellular_component | cytoplasm |
| B | 0005739 | cellular_component | mitochondrion |
| B | 0005791 | cellular_component | rough endoplasmic reticulum |
| B | 0005829 | cellular_component | cytosol |
| B | 0005929 | cellular_component | cilium |
| B | 0006096 | biological_process | glycolytic process |
| B | 0006417 | biological_process | regulation of translation |
| B | 0012501 | biological_process | programmed cell death |
| B | 0016301 | molecular_function | kinase activity |
| B | 0023026 | molecular_function | MHC class II protein complex binding |
| B | 0030955 | molecular_function | potassium ion binding |
| B | 0031982 | cellular_component | vesicle |
| B | 0032869 | biological_process | cellular response to insulin stimulus |
| B | 0034774 | cellular_component | secretory granule lumen |
| B | 0045296 | molecular_function | cadherin binding |
| B | 0046872 | molecular_function | metal ion binding |
| B | 0061621 | biological_process | canonical glycolysis |
| B | 0062023 | cellular_component | collagen-containing extracellular matrix |
| B | 0070062 | cellular_component | extracellular exosome |
| B | 1903561 | cellular_component | extracellular vesicle |
| B | 1903672 | biological_process | positive regulation of sprouting angiogenesis |
| B | 1904813 | cellular_component | ficolin-1-rich granule lumen |
| B | 2000767 | biological_process | positive regulation of cytoplasmic translation |
Functional Information from PDB Data
| site_id | AC1 |
| Number of Residues | 12 |
| Details | binding site for residue SER A 601 |
| Chain | Residue |
| A | ARG43 |
| A | HOH805 |
| A | HOH818 |
| A | HOH850 |
| A | ASN44 |
| A | ASN70 |
| A | ARG106 |
| A | HIS464 |
| A | ILE469 |
| A | PHE470 |
| A | PRO471 |
| A | HOH760 |
| site_id | AC2 |
| Number of Residues | 5 |
| Details | binding site for residue MG A 602 |
| Chain | Residue |
| A | GLU272 |
| A | ASP296 |
| A | OXL603 |
| A | HOH774 |
| A | HOH881 |
| site_id | AC3 |
| Number of Residues | 11 |
| Details | binding site for residue OXL A 603 |
| Chain | Residue |
| A | LYS270 |
| A | GLU272 |
| A | ALA293 |
| A | ARG294 |
| A | GLY295 |
| A | ASP296 |
| A | THR328 |
| A | MG602 |
| A | HOH774 |
| A | HOH778 |
| A | HOH881 |
| site_id | AC4 |
| Number of Residues | 7 |
| Details | binding site for residue K A 604 |
| Chain | Residue |
| A | ASN75 |
| A | SER77 |
| A | ASP113 |
| A | THR114 |
| A | SER243 |
| A | HOH886 |
| A | HOH1060 |
| site_id | AC5 |
| Number of Residues | 2 |
| Details | binding site for residue SCN A 605 |
| Chain | Residue |
| A | LYS322 |
| A | HOH790 |
| site_id | AC6 |
| Number of Residues | 5 |
| Details | binding site for residue SCN A 606 |
| Chain | Residue |
| A | LYS266 |
| A | HIS439 |
| A | LEU465 |
| A | TYR466 |
| A | HOH845 |
| site_id | AC7 |
| Number of Residues | 8 |
| Details | binding site for residue PEG A 607 |
| Chain | Residue |
| A | HIS252 |
| A | ALA286 |
| A | LYS505 |
| A | GLY506 |
| A | VAL530 |
| A | HOH731 |
| A | HOH844 |
| A | HOH892 |
| site_id | AC8 |
| Number of Residues | 7 |
| Details | binding site for residue B3P A 608 |
| Chain | Residue |
| A | ASP177 |
| A | LEU180 |
| A | LYS207 |
| A | GLN329 |
| A | GLU332 |
| A | GLY363 |
| A | HOH862 |
| site_id | AC9 |
| Number of Residues | 12 |
| Details | binding site for residue SER B 601 |
| Chain | Residue |
| B | ARG43 |
| B | ASN44 |
| B | ASN70 |
| B | ARG106 |
| B | HIS464 |
| B | ILE469 |
| B | PHE470 |
| B | PRO471 |
| B | HOH730 |
| B | HOH789 |
| B | HOH845 |
| B | HOH869 |
| site_id | AD1 |
| Number of Residues | 5 |
| Details | binding site for residue MG B 602 |
| Chain | Residue |
| B | GLU272 |
| B | ASP296 |
| B | OXL603 |
| B | HOH800 |
| B | HOH872 |
| site_id | AD2 |
| Number of Residues | 11 |
| Details | binding site for residue OXL B 603 |
| Chain | Residue |
| B | LYS270 |
| B | GLU272 |
| B | ALA293 |
| B | ARG294 |
| B | GLY295 |
| B | ASP296 |
| B | THR328 |
| B | MG602 |
| B | HOH729 |
| B | HOH800 |
| B | HOH872 |
| site_id | AD3 |
| Number of Residues | 7 |
| Details | binding site for residue K B 604 |
| Chain | Residue |
| B | ASN75 |
| B | SER77 |
| B | ASP113 |
| B | THR114 |
| B | SER243 |
| B | HOH767 |
| B | HOH1092 |
| site_id | AD4 |
| Number of Residues | 6 |
| Details | binding site for residue SCN B 605 |
| Chain | Residue |
| B | LYS266 |
| B | PRO323 |
| B | HIS439 |
| B | LEU465 |
| B | TYR466 |
| B | HOH867 |
| site_id | AD5 |
| Number of Residues | 5 |
| Details | binding site for residue SCN B 606 |
| Chain | Residue |
| B | HIS274 |
| B | PRO302 |
| B | LYS305 |
| B | HOH756 |
| A | ILE35 |
| site_id | AD6 |
| Number of Residues | 5 |
| Details | binding site for residue SCN B 607 |
| Chain | Residue |
| A | HIS81 |
| A | GLU82 |
| B | HIS252 |
| B | ARG255 |
| B | ALA286 |
| site_id | AD7 |
| Number of Residues | 14 |
| Details | binding site for residue PG4 B 608 |
| Chain | Residue |
| A | PHE26 |
| A | HOH951 |
| A | HOH954 |
| A | HOH993 |
| B | PHE26 |
| B | LEU353 |
| B | EDO609 |
| B | HOH713 |
| B | HOH715 |
| B | HOH754 |
| B | HOH881 |
| B | HOH948 |
| B | HOH983 |
| B | HOH1135 |
| site_id | AD8 |
| Number of Residues | 6 |
| Details | binding site for residue EDO B 609 |
| Chain | Residue |
| A | HOH993 |
| B | PHE26 |
| B | LEU353 |
| B | ALA388 |
| B | PG4608 |
| B | HOH710 |
| site_id | AD9 |
| Number of Residues | 12 |
| Details | binding site for residue B3P B 610 |
| Chain | Residue |
| A | LYS337 |
| B | ASP177 |
| B | ASP178 |
| B | LEU180 |
| B | LYS207 |
| B | GLN329 |
| B | GLU332 |
| B | GLY363 |
| B | HOH773 |
| B | HOH776 |
| B | HOH795 |
| B | HOH821 |
Functional Information from PROSITE/UniProt
| site_id | PS00110 |
| Number of Residues | 13 |
| Details | PYRUVATE_KINASE Pyruvate kinase active site signature. IkIISKIENhEGV |
| Chain | Residue | Details |
| A | ILE265-VAL277 |
Functional Information from SwissProt/UniProt
| site_id | SWS_FT_FI1 |
| Number of Residues | 6 |
| Details | BINDING: BINDING => ECO:0000269|PubMed:23064226 |
| Chain | Residue | Details |
| A | ASN70 | |
| A | ARG106 | |
| A | HIS464 | |
| B | ASN70 | |
| B | ARG106 | |
| B | HIS464 |
| site_id | SWS_FT_FI2 |
| Number of Residues | 10 |
| Details | BINDING: BINDING => ECO:0000250|UniProtKB:P30613 |
| Chain | Residue | Details |
| A | ARG73 | |
| B | THR328 | |
| A | LYS270 | |
| A | GLY295 | |
| A | ASP296 | |
| A | THR328 | |
| B | ARG73 | |
| B | LYS270 | |
| B | GLY295 | |
| B | ASP296 |
| site_id | SWS_FT_FI3 |
| Number of Residues | 14 |
| Details | BINDING: BINDING => ECO:0000269|PubMed:23530218, ECO:0007744|PDB:4FXF |
| Chain | Residue | Details |
| A | ASN75 | |
| B | ASP113 | |
| B | THR114 | |
| B | ARG120 | |
| B | LYS207 | |
| B | GLU272 | |
| A | SER77 | |
| A | ASP113 | |
| A | THR114 | |
| A | ARG120 | |
| A | LYS207 | |
| A | GLU272 | |
| B | ASN75 | |
| B | SER77 |
| site_id | SWS_FT_FI4 |
| Number of Residues | 8 |
| Details | BINDING: BINDING => ECO:0000269|PubMed:15996096, ECO:0000269|PubMed:23530218, ECO:0007744|PDB:1T5A, ECO:0007744|PDB:4FXF |
| Chain | Residue | Details |
| A | THR432 | |
| A | TRP482 | |
| A | ARG489 | |
| A | ARG516 | |
| B | THR432 | |
| B | TRP482 | |
| B | ARG489 | |
| B | ARG516 |
| site_id | SWS_FT_FI5 |
| Number of Residues | 2 |
| Details | SITE: Transition state stabilizer => ECO:0000250|UniProtKB:P00549 |
| Chain | Residue | Details |
| A | LYS270 | |
| B | LYS270 |
| site_id | SWS_FT_FI6 |
| Number of Residues | 2 |
| Details | SITE: Crucial for phosphotyrosine binding => ECO:0000269|PubMed:27199445 |
| Chain | Residue | Details |
| A | LYS433 | |
| B | LYS433 |
| site_id | SWS_FT_FI7 |
| Number of Residues | 2 |
| Details | MOD_RES: N-acetylserine => ECO:0000269|Ref.11, ECO:0007744|PubMed:19413330, ECO:0007744|PubMed:25944712 |
| Chain | Residue | Details |
| A | SER2 | |
| B | SER2 |
| site_id | SWS_FT_FI8 |
| Number of Residues | 2 |
| Details | MOD_RES: N6,N6,N6-trimethyllysine => ECO:0007744|PubMed:24129315 |
| Chain | Residue | Details |
| A | LYS3 | |
| B | LYS3 |
| site_id | SWS_FT_FI9 |
| Number of Residues | 2 |
| Details | MOD_RES: Phosphoserine => ECO:0007744|PubMed:16964243, ECO:0007744|PubMed:17081983, ECO:0007744|PubMed:18088087, ECO:0007744|PubMed:18669648, ECO:0007744|PubMed:18691976, ECO:0007744|PubMed:19690332, ECO:0007744|PubMed:20068231, ECO:0007744|PubMed:21406692, ECO:0007744|PubMed:23186163, ECO:0007744|PubMed:24275569 |
| Chain | Residue | Details |
| A | SER37 | |
| B | SER37 |
| site_id | SWS_FT_FI10 |
| Number of Residues | 2 |
| Details | MOD_RES: Phosphothreonine => ECO:0007744|PubMed:23186163 |
| Chain | Residue | Details |
| A | THR41 | |
| B | THR41 |
| site_id | SWS_FT_FI11 |
| Number of Residues | 4 |
| Details | MOD_RES: N6-acetyllysine => ECO:0007744|PubMed:19608861 |
| Chain | Residue | Details |
| A | LYS62 | |
| A | LYS89 | |
| B | LYS62 | |
| B | LYS89 |
| site_id | SWS_FT_FI12 |
| Number of Residues | 4 |
| Details | MOD_RES: N6-succinyllysine => ECO:0000250|UniProtKB:P52480 |
| Chain | Residue | Details |
| A | LYS66 | |
| A | LYS498 | |
| B | LYS66 | |
| B | LYS498 |
| site_id | SWS_FT_FI13 |
| Number of Residues | 4 |
| Details | MOD_RES: Phosphoserine => ECO:0000250|UniProtKB:P11980 |
| Chain | Residue | Details |
| A | SER97 | |
| A | SER100 | |
| B | SER97 | |
| B | SER100 |
| site_id | SWS_FT_FI14 |
| Number of Residues | 2 |
| Details | MOD_RES: Phosphotyrosine => ECO:0007744|PubMed:15592455, ECO:0007744|PubMed:23186163 |
| Chain | Residue | Details |
| A | TYR105 | |
| B | TYR105 |
| site_id | SWS_FT_FI15 |
| Number of Residues | 2 |
| Details | MOD_RES: Phosphoserine => ECO:0007744|PubMed:23186163 |
| Chain | Residue | Details |
| A | SER127 | |
| B | SER127 |
| site_id | SWS_FT_FI16 |
| Number of Residues | 2 |
| Details | MOD_RES: Phosphotyrosine => ECO:0000250|UniProtKB:P52480 |
| Chain | Residue | Details |
| A | TYR148 | |
| B | TYR148 |
| site_id | SWS_FT_FI17 |
| Number of Residues | 4 |
| Details | MOD_RES: N6-succinyllysine; alternate => ECO:0000250|UniProtKB:P52480 |
| Chain | Residue | Details |
| A | LYS166 | |
| A | LYS322 | |
| B | LYS166 | |
| B | LYS322 |
| site_id | SWS_FT_FI18 |
| Number of Residues | 2 |
| Details | MOD_RES: Phosphotyrosine => ECO:0007744|PubMed:19690332 |
| Chain | Residue | Details |
| A | TYR175 | |
| B | TYR175 |
| site_id | SWS_FT_FI19 |
| Number of Residues | 2 |
| Details | MOD_RES: Phosphothreonine => ECO:0007744|PubMed:19690332 |
| Chain | Residue | Details |
| A | THR195 | |
| B | THR195 |
| site_id | SWS_FT_FI20 |
| Number of Residues | 2 |
| Details | MOD_RES: N6-acetyllysine; alternate => ECO:0007744|PubMed:19608861 |
| Chain | Residue | Details |
| A | LYS266 | |
| B | LYS266 |
| site_id | SWS_FT_FI21 |
| Number of Residues | 2 |
| Details | MOD_RES: N6-acetyllysine; alternate => ECO:0000250|UniProtKB:P52480 |
| Chain | Residue | Details |
| A | LYS270 | |
| B | LYS270 |
| site_id | SWS_FT_FI22 |
| Number of Residues | 2 |
| Details | MOD_RES: N6-acetyllysine => ECO:0000269|PubMed:21700219 |
| Chain | Residue | Details |
| A | LYS305 | |
| B | LYS305 |
| site_id | SWS_FT_FI23 |
| Number of Residues | 4 |
| Details | MOD_RES: 4-hydroxyproline => ECO:0000269|PubMed:21620138 |
| Chain | Residue | Details |
| A | PRO403 | |
| A | PRO408 | |
| B | PRO403 | |
| B | PRO408 |
| site_id | SWS_FT_FI24 |
| Number of Residues | 4 |
| Details | MOD_RES: S-nitrosocysteine => ECO:0000269|PubMed:30487609 |
| Chain | Residue | Details |
| A | CYS423 | |
| A | CYS424 | |
| B | CYS423 | |
| B | CYS424 |
| site_id | SWS_FT_FI25 |
| Number of Residues | 2 |
| Details | MOD_RES: N6-acetyllysine => ECO:0000269|PubMed:24120661, ECO:0000269|PubMed:26787900, ECO:0007744|PubMed:19608861 |
| Chain | Residue | Details |
| A | LYS433 | |
| B | LYS433 |
| site_id | SWS_FT_FI26 |
| Number of Residues | 2 |
| Details | MOD_RES: N6-acetyllysine => ECO:0000250|UniProtKB:P52480 |
| Chain | Residue | Details |
| A | LYS475 | |
| B | LYS475 |
| site_id | SWS_FT_FI27 |
| Number of Residues | 2 |
| Details | CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2) => ECO:0007744|PubMed:28112733 |
| Chain | Residue | Details |
| A | LYS115 | |
| B | LYS115 |
| site_id | SWS_FT_FI28 |
| Number of Residues | 6 |
| Details | CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2); alternate => ECO:0007744|PubMed:28112733 |
| Chain | Residue | Details |
| A | LYS266 | |
| A | LYS270 | |
| B | LYS266 | |
| B | LYS270 |
| site_id | SWS_FT_FI29 |
| Number of Residues | 2 |
| Details | CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO1); alternate => ECO:0007744|PubMed:25114211 |
| Chain | Residue | Details |
| A | LYS166 | |
| B | LYS166 |
