4F7I
Structure of Isopropylmalate dehydrogenase from Thermus thermophilus in complex with IPM, Mn and NADH
Functional Information from GO Data
Chain | GOid | namespace | contents |
A | 0000287 | molecular_function | magnesium ion binding |
A | 0003862 | molecular_function | 3-isopropylmalate dehydrogenase activity |
A | 0005737 | cellular_component | cytoplasm |
A | 0009098 | biological_process | L-leucine biosynthetic process |
A | 0016491 | molecular_function | oxidoreductase activity |
A | 0016616 | molecular_function | oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor |
A | 0042802 | molecular_function | identical protein binding |
A | 0046872 | molecular_function | metal ion binding |
A | 0051287 | molecular_function | NAD binding |
B | 0000287 | molecular_function | magnesium ion binding |
B | 0003862 | molecular_function | 3-isopropylmalate dehydrogenase activity |
B | 0005737 | cellular_component | cytoplasm |
B | 0009098 | biological_process | L-leucine biosynthetic process |
B | 0016491 | molecular_function | oxidoreductase activity |
B | 0016616 | molecular_function | oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor |
B | 0042802 | molecular_function | identical protein binding |
B | 0046872 | molecular_function | metal ion binding |
B | 0051287 | molecular_function | NAD binding |
C | 0000287 | molecular_function | magnesium ion binding |
C | 0003862 | molecular_function | 3-isopropylmalate dehydrogenase activity |
C | 0005737 | cellular_component | cytoplasm |
C | 0009098 | biological_process | L-leucine biosynthetic process |
C | 0016491 | molecular_function | oxidoreductase activity |
C | 0016616 | molecular_function | oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor |
C | 0042802 | molecular_function | identical protein binding |
C | 0046872 | molecular_function | metal ion binding |
C | 0051287 | molecular_function | NAD binding |
D | 0000287 | molecular_function | magnesium ion binding |
D | 0003862 | molecular_function | 3-isopropylmalate dehydrogenase activity |
D | 0005737 | cellular_component | cytoplasm |
D | 0009098 | biological_process | L-leucine biosynthetic process |
D | 0016491 | molecular_function | oxidoreductase activity |
D | 0016616 | molecular_function | oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor |
D | 0042802 | molecular_function | identical protein binding |
D | 0046872 | molecular_function | metal ion binding |
D | 0051287 | molecular_function | NAD binding |
Functional Information from PDB Data
site_id | AC1 |
Number of Residues | 13 |
Details | BINDING SITE FOR RESIDUE IPM A 800 |
Chain | Residue |
A | ARG94 |
B | LYS185 |
B | VAL188 |
B | ASP217 |
B | HOH2013 |
A | ARG104 |
A | ARG132 |
A | TYR139 |
A | ASP241 |
A | NAD900 |
A | MN999 |
A | HOH2002 |
A | HOH2022 |
site_id | AC2 |
Number of Residues | 34 |
Details | BINDING SITE FOR RESIDUE NAD A 900 |
Chain | Residue |
A | ILE11 |
A | SER71 |
A | VAL72 |
A | GLY73 |
A | GLY74 |
A | GLU87 |
A | LEU90 |
A | LEU254 |
A | GLU270 |
A | HIS273 |
A | GLY274 |
A | SER275 |
A | ALA276 |
A | PRO277 |
A | ASP278 |
A | ILE279 |
A | ASN286 |
A | IPM800 |
A | K1001 |
A | GOL1003 |
A | GOL1005 |
A | HOH2004 |
A | HOH2006 |
A | HOH2022 |
A | HOH2023 |
A | HOH2033 |
A | HOH2044 |
A | HOH2076 |
A | HOH2086 |
A | HOH2100 |
B | ASN187 |
B | TYR215 |
B | ALA218 |
B | HIS222 |
site_id | AC3 |
Number of Residues | 5 |
Details | BINDING SITE FOR RESIDUE MPO A 950 |
Chain | Residue |
A | LYS175 |
A | ARG176 |
A | GLU299 |
A | HIS300 |
A | GOL1009 |
site_id | AC4 |
Number of Residues | 5 |
Details | BINDING SITE FOR RESIDUE MN A 999 |
Chain | Residue |
A | ASP241 |
A | IPM800 |
A | HOH2001 |
A | HOH2002 |
B | ASP217 |
site_id | AC5 |
Number of Residues | 6 |
Details | BINDING SITE FOR RESIDUE K A 1001 |
Chain | Residue |
A | GLY70 |
A | SER71 |
A | GLU270 |
A | PRO271 |
A | HIS273 |
A | NAD900 |
site_id | AC6 |
Number of Residues | 3 |
Details | BINDING SITE FOR RESIDUE K A 1002 |
Chain | Residue |
A | GLU62 |
A | ALA64 |
A | THR266 |
site_id | AC7 |
Number of Residues | 8 |
Details | BINDING SITE FOR RESIDUE GOL A 1003 |
Chain | Residue |
A | GLY73 |
A | GLY74 |
A | TRP77 |
A | ASP78 |
A | ARG85 |
A | GLU87 |
A | NAD900 |
B | TYR215 |
site_id | AC8 |
Number of Residues | 11 |
Details | BINDING SITE FOR RESIDUE GOL A 1004 |
Chain | Residue |
A | GLU155 |
A | TYR157 |
A | VAL183 |
A | VAL191 |
A | GLY192 |
A | TRP195 |
A | THR235 |
A | GLY236 |
A | PHE239 |
A | HOH2018 |
A | HOH2068 |
site_id | AC9 |
Number of Residues | 8 |
Details | BINDING SITE FOR RESIDUE GOL A 1005 |
Chain | Residue |
A | SER253 |
A | LEU254 |
A | ASP326 |
A | NAD900 |
A | HOH2100 |
B | MET221 |
B | ARG225 |
B | HOH2038 |
site_id | BC1 |
Number of Residues | 6 |
Details | BINDING SITE FOR RESIDUE GOL A 1006 |
Chain | Residue |
A | LYS95 |
A | GLY136 |
A | GLY137 |
A | ARG156 |
A | GLU161 |
A | HOH2039 |
site_id | BC2 |
Number of Residues | 8 |
Details | BINDING SITE FOR RESIDUE GOL A 1007 |
Chain | Residue |
A | LYS107 |
A | VAL108 |
A | PHE109 |
A | LEU112 |
A | PRO251 |
A | LEU319 |
A | GOL1008 |
A | HOH2064 |
site_id | BC3 |
Number of Residues | 7 |
Details | BINDING SITE FOR RESIDUE GOL A 1008 |
Chain | Residue |
A | PRO105 |
A | ALA106 |
A | LYS107 |
A | PHE109 |
A | LEU256 |
A | GOL1007 |
A | GOL1009 |
site_id | BC4 |
Number of Residues | 6 |
Details | BINDING SITE FOR RESIDUE GOL A 1009 |
Chain | Residue |
A | ALA295 |
A | MET296 |
A | GLU299 |
A | GLU312 |
A | MPO950 |
A | GOL1008 |
site_id | BC5 |
Number of Residues | 2 |
Details | BINDING SITE FOR RESIDUE GOL A 1010 |
Chain | Residue |
A | GLY263 |
A | GOL1011 |
site_id | BC6 |
Number of Residues | 4 |
Details | BINDING SITE FOR RESIDUE GOL A 1011 |
Chain | Residue |
A | ARG164 |
A | ARG167 |
A | GLU171 |
A | GOL1010 |
site_id | BC7 |
Number of Residues | 4 |
Details | BINDING SITE FOR RESIDUE EOH A 1012 |
Chain | Residue |
A | MET221 |
A | ARG225 |
B | SER253 |
B | LEU254 |
site_id | BC8 |
Number of Residues | 12 |
Details | BINDING SITE FOR RESIDUE IPM B 800 |
Chain | Residue |
A | LYS185 |
A | ASP217 |
A | HOH2013 |
B | LEU91 |
B | ARG94 |
B | ARG104 |
B | ARG132 |
B | TYR139 |
B | ASP241 |
B | NAD900 |
B | MN999 |
B | HOH2021 |
site_id | BC9 |
Number of Residues | 31 |
Details | BINDING SITE FOR RESIDUE NAD B 900 |
Chain | Residue |
A | ASN187 |
A | TYR215 |
A | ALA218 |
A | HOH2061 |
B | ILE11 |
B | SER71 |
B | VAL72 |
B | GLY73 |
B | GLY74 |
B | GLU87 |
B | LEU90 |
B | LEU254 |
B | GLU270 |
B | VAL272 |
B | HIS273 |
B | GLY274 |
B | SER275 |
B | ALA276 |
B | PRO277 |
B | ASP278 |
B | ILE279 |
B | ASN286 |
B | IPM800 |
B | K1001 |
B | GOL1004 |
B | HOH2009 |
B | HOH2016 |
B | HOH2021 |
B | HOH2035 |
B | HOH2044 |
B | HOH2046 |
site_id | CC1 |
Number of Residues | 5 |
Details | BINDING SITE FOR RESIDUE MN B 999 |
Chain | Residue |
A | ASP217 |
B | ASP241 |
B | IPM800 |
B | HOH2001 |
B | HOH2002 |
site_id | CC2 |
Number of Residues | 6 |
Details | BINDING SITE FOR RESIDUE K B 1001 |
Chain | Residue |
B | GLY70 |
B | SER71 |
B | GLU270 |
B | PRO271 |
B | HIS273 |
B | NAD900 |
site_id | CC3 |
Number of Residues | 5 |
Details | BINDING SITE FOR RESIDUE K B 1002 |
Chain | Residue |
B | GLU62 |
B | ALA64 |
B | THR266 |
B | HOH2050 |
B | HOH2051 |
site_id | CC4 |
Number of Residues | 9 |
Details | BINDING SITE FOR RESIDUE GOL B 1003 |
Chain | Residue |
B | GLU155 |
B | TYR157 |
B | VAL183 |
B | TRP195 |
B | THR235 |
B | GLY236 |
B | PHE239 |
B | HOH2037 |
B | HOH2098 |
site_id | CC5 |
Number of Residues | 10 |
Details | BINDING SITE FOR RESIDUE GOL B 1004 |
Chain | Residue |
A | TYR215 |
B | GLY73 |
B | GLY74 |
B | TRP77 |
B | ASP78 |
B | ARG85 |
B | GLU87 |
B | NAD900 |
B | HOH2093 |
B | HOH2108 |
site_id | CC6 |
Number of Residues | 9 |
Details | BINDING SITE FOR RESIDUE GOL B 1005 |
Chain | Residue |
A | PRO143 |
A | ARG156 |
B | ASP47 |
B | LYS76 |
B | TRP77 |
B | LEU80 |
B | PRO143 |
B | TRP152 |
B | HOH2024 |
site_id | CC7 |
Number of Residues | 6 |
Details | BINDING SITE FOR RESIDUE GOL B 1006 |
Chain | Residue |
B | LYS107 |
B | VAL108 |
B | PHE109 |
B | PRO251 |
B | GOL1007 |
B | HOH2057 |
site_id | CC8 |
Number of Residues | 8 |
Details | BINDING SITE FOR RESIDUE GOL B 1007 |
Chain | Residue |
B | PRO105 |
B | ALA106 |
B | LYS107 |
B | LEU256 |
B | LEU257 |
B | LEU292 |
B | GOL1006 |
B | GOL1008 |
site_id | CC9 |
Number of Residues | 5 |
Details | BINDING SITE FOR RESIDUE GOL B 1008 |
Chain | Residue |
B | PRO105 |
B | ALA295 |
B | MET296 |
B | GLU312 |
B | GOL1007 |
site_id | DC1 |
Number of Residues | 3 |
Details | BINDING SITE FOR RESIDUE EOH B 1009 |
Chain | Residue |
B | PRO7 |
B | PRO13 |
B | GLU17 |
site_id | DC2 |
Number of Residues | 7 |
Details | BINDING SITE FOR RESIDUE GOL B 1010 |
Chain | Residue |
B | GLU200 |
B | GLY203 |
B | TYR206 |
B | VAL209 |
B | LEU211 |
B | HOH2080 |
B | HOH2117 |
site_id | DC3 |
Number of Residues | 15 |
Details | BINDING SITE FOR RESIDUE IPM C 800 |
Chain | Residue |
C | LEU90 |
C | LEU91 |
C | ARG94 |
C | ARG104 |
C | ARG132 |
C | TYR139 |
C | ASP241 |
C | NAD900 |
C | MN999 |
C | HOH2001 |
C | HOH2014 |
D | LYS185 |
D | VAL188 |
D | ASP217 |
D | HOH2007 |
site_id | DC4 |
Number of Residues | 31 |
Details | BINDING SITE FOR RESIDUE NAD C 900 |
Chain | Residue |
C | ILE11 |
C | SER71 |
C | VAL72 |
C | GLY73 |
C | GLY74 |
C | GLU87 |
C | LEU90 |
C | LEU254 |
C | GLU270 |
C | VAL272 |
C | HIS273 |
C | GLY274 |
C | SER275 |
C | ALA276 |
C | PRO277 |
C | ASP278 |
C | ILE279 |
C | ASN286 |
C | IPM800 |
C | K1001 |
C | GOL1004 |
C | HOH2004 |
C | HOH2011 |
C | HOH2014 |
C | HOH2031 |
C | HOH2056 |
C | HOH2057 |
D | ASN187 |
D | TYR215 |
D | ALA218 |
D | HOH2029 |
site_id | DC5 |
Number of Residues | 7 |
Details | BINDING SITE FOR RESIDUE MPO C 950 |
Chain | Residue |
C | LEU103 |
C | LYS175 |
C | ARG176 |
C | MET296 |
C | GLU299 |
C | HIS300 |
C | GOL1005 |
site_id | DC6 |
Number of Residues | 5 |
Details | BINDING SITE FOR RESIDUE MN C 999 |
Chain | Residue |
C | ASP241 |
C | IPM800 |
C | HOH2001 |
C | HOH2002 |
D | ASP217 |
site_id | DC7 |
Number of Residues | 6 |
Details | BINDING SITE FOR RESIDUE K C 1001 |
Chain | Residue |
C | GLY70 |
C | SER71 |
C | GLU270 |
C | PRO271 |
C | HIS273 |
C | NAD900 |
site_id | DC8 |
Number of Residues | 4 |
Details | BINDING SITE FOR RESIDUE K C 1002 |
Chain | Residue |
C | GLU62 |
C | ALA64 |
C | THR266 |
C | HOH2098 |
site_id | DC9 |
Number of Residues | 11 |
Details | BINDING SITE FOR RESIDUE GOL C 1003 |
Chain | Residue |
C | GLU155 |
C | TYR157 |
C | VAL183 |
C | VAL191 |
C | GLY192 |
C | TRP195 |
C | THR235 |
C | GLY236 |
C | PHE239 |
C | HOH2043 |
C | HOH2044 |
site_id | EC1 |
Number of Residues | 10 |
Details | BINDING SITE FOR RESIDUE GOL C 1004 |
Chain | Residue |
C | GLY73 |
C | GLY74 |
C | TRP77 |
C | ASP78 |
C | ARG85 |
C | GLU87 |
C | NAD900 |
C | HOH2087 |
C | HOH2118 |
D | TYR215 |
site_id | EC2 |
Number of Residues | 5 |
Details | BINDING SITE FOR RESIDUE GOL C 1005 |
Chain | Residue |
C | MET296 |
C | GLU299 |
C | GLU312 |
C | MPO950 |
C | GOL1006 |
site_id | EC3 |
Number of Residues | 6 |
Details | BINDING SITE FOR RESIDUE GOL C 1006 |
Chain | Residue |
C | PRO105 |
C | LYS107 |
C | PHE109 |
C | PRO258 |
C | GOL1005 |
C | GOL1007 |
site_id | EC4 |
Number of Residues | 7 |
Details | BINDING SITE FOR RESIDUE GOL C 1007 |
Chain | Residue |
C | LYS107 |
C | VAL108 |
C | PHE109 |
C | PRO251 |
C | LEU292 |
C | GOL1006 |
C | HOH2075 |
site_id | EC5 |
Number of Residues | 1 |
Details | BINDING SITE FOR RESIDUE GOL C 1018 |
Chain | Residue |
C | GOL1008 |
site_id | EC6 |
Number of Residues | 7 |
Details | BINDING SITE FOR RESIDUE GOL C 1008 |
Chain | Residue |
C | GLU171 |
C | ARG174 |
C | GLY205 |
C | ILE284 |
C | SER330 |
C | GOL1018 |
C | HOH2109 |
site_id | EC7 |
Number of Residues | 4 |
Details | BINDING SITE FOR RESIDUE EOH C 1009 |
Chain | Residue |
C | GLU148 |
C | HOH2110 |
D | LYS159 |
D | PHE194 |
site_id | EC8 |
Number of Residues | 4 |
Details | BINDING SITE FOR RESIDUE EOH C 1010 |
Chain | Residue |
C | GLY79 |
C | LEU80 |
C | ARG85 |
C | HOH2118 |
site_id | EC9 |
Number of Residues | 14 |
Details | BINDING SITE FOR RESIDUE IPM D 800 |
Chain | Residue |
C | LYS185 |
C | ASP217 |
C | HOH2017 |
D | LEU90 |
D | LEU91 |
D | ARG94 |
D | ARG104 |
D | ARG132 |
D | TYR139 |
D | ASP241 |
D | NAD900 |
D | MN999 |
D | HOH2002 |
D | HOH2016 |
site_id | FC1 |
Number of Residues | 30 |
Details | BINDING SITE FOR RESIDUE NAD D 900 |
Chain | Residue |
C | ASN187 |
C | TYR215 |
C | ALA218 |
C | HOH2027 |
D | ILE11 |
D | SER71 |
D | VAL72 |
D | GLY73 |
D | GLY74 |
D | GLU87 |
D | LEU90 |
D | LEU254 |
D | GLU270 |
D | HIS273 |
D | GLY274 |
D | SER275 |
D | ALA276 |
D | PRO277 |
D | ASP278 |
D | ILE279 |
D | ASN286 |
D | IPM800 |
D | K1001 |
D | GOL1004 |
D | HOH2003 |
D | HOH2006 |
D | HOH2016 |
D | HOH2021 |
D | HOH2048 |
D | HOH2067 |
site_id | FC2 |
Number of Residues | 8 |
Details | BINDING SITE FOR RESIDUE MPO D 950 |
Chain | Residue |
D | LEU103 |
D | ALA172 |
D | LYS175 |
D | ARG176 |
D | MET296 |
D | GLU299 |
D | HIS300 |
D | GOL1007 |
site_id | FC3 |
Number of Residues | 5 |
Details | BINDING SITE FOR RESIDUE MN D 999 |
Chain | Residue |
C | ASP217 |
D | ASP241 |
D | IPM800 |
D | HOH2001 |
D | HOH2002 |
site_id | FC4 |
Number of Residues | 6 |
Details | BINDING SITE FOR RESIDUE K D 1001 |
Chain | Residue |
D | GLY70 |
D | SER71 |
D | GLU270 |
D | PRO271 |
D | HIS273 |
D | NAD900 |
site_id | FC5 |
Number of Residues | 11 |
Details | BINDING SITE FOR RESIDUE GOL D 1003 |
Chain | Residue |
D | GLU155 |
D | TYR157 |
D | VAL183 |
D | VAL191 |
D | GLY192 |
D | TRP195 |
D | THR235 |
D | GLY236 |
D | PHE239 |
D | HOH2017 |
D | HOH2036 |
site_id | FC6 |
Number of Residues | 9 |
Details | BINDING SITE FOR RESIDUE GOL D 1004 |
Chain | Residue |
C | TYR215 |
D | GLY73 |
D | GLY74 |
D | TRP77 |
D | ASP78 |
D | ARG85 |
D | GLU87 |
D | NAD900 |
D | HOH2066 |
site_id | FC7 |
Number of Residues | 10 |
Details | BINDING SITE FOR RESIDUE GOL D 1005 |
Chain | Residue |
C | ASP47 |
C | LYS76 |
C | TRP77 |
C | LEU80 |
C | PRO143 |
C | TRP152 |
D | PRO143 |
D | THR154 |
D | ARG156 |
D | HOH2023 |
site_id | FC8 |
Number of Residues | 8 |
Details | BINDING SITE FOR RESIDUE GOL D 1006 |
Chain | Residue |
D | LYS107 |
D | VAL108 |
D | PHE109 |
D | LEU112 |
D | PRO251 |
D | LEU319 |
D | GOL1008 |
D | HOH2057 |
site_id | FC9 |
Number of Residues | 4 |
Details | BINDING SITE FOR RESIDUE GOL D 1007 |
Chain | Residue |
D | MET296 |
D | GLU299 |
D | MPO950 |
D | GOL1008 |
site_id | GC1 |
Number of Residues | 8 |
Details | BINDING SITE FOR RESIDUE GOL D 1008 |
Chain | Residue |
D | PRO105 |
D | ALA106 |
D | LYS107 |
D | LEU256 |
D | LEU257 |
D | LEU292 |
D | GOL1006 |
D | GOL1007 |
site_id | GC2 |
Number of Residues | 4 |
Details | BINDING SITE FOR RESIDUE EOH D 1009 |
Chain | Residue |
C | SER253 |
C | LEU254 |
D | MET221 |
D | ARG225 |
site_id | GC3 |
Number of Residues | 5 |
Details | BINDING SITE FOR RESIDUE EOH D 1010 |
Chain | Residue |
C | MET221 |
D | SER253 |
D | LEU254 |
D | HOH2081 |
D | HOH2082 |
Functional Information from PROSITE/UniProt
site_id | PS00470 |
Number of Residues | 20 |
Details | IDH_IMDH Isocitrate and isopropylmalate dehydrogenases signature. NIFGDIlSDlaSvlp.GSLGL |
Chain | Residue | Details |
A | ASN237-LEU256 |
Functional Information from SwissProt/UniProt
site_id | SWS_FT_FI1 |
Number of Residues | 8 |
Details | BINDING: BINDING => ECO:0000269|PubMed:7881901 |
Chain | Residue | Details |
A | GLY74 | |
A | GLY274 | |
B | GLY74 | |
B | GLY274 | |
C | GLY74 | |
C | GLY274 | |
D | GLY74 | |
D | GLY274 |
site_id | SWS_FT_FI2 |
Number of Residues | 24 |
Details | BINDING: BINDING => ECO:0000250 |
Chain | Residue | Details |
A | ARG94 | |
B | ASP217 | |
B | ASP241 | |
B | ASP245 | |
C | ARG94 | |
C | ARG104 | |
C | ARG132 | |
C | ASP217 | |
C | ASP241 | |
C | ASP245 | |
D | ARG94 | |
A | ARG104 | |
D | ARG104 | |
D | ARG132 | |
D | ASP217 | |
D | ASP241 | |
D | ASP245 | |
A | ARG132 | |
A | ASP217 | |
A | ASP241 | |
A | ASP245 | |
B | ARG94 | |
B | ARG104 | |
B | ARG132 |
site_id | SWS_FT_FI3 |
Number of Residues | 4 |
Details | SITE: Important for catalysis |
Chain | Residue | Details |
A | TYR139 | |
B | TYR139 | |
C | TYR139 | |
D | TYR139 |
site_id | SWS_FT_FI4 |
Number of Residues | 4 |
Details | SITE: Important for catalysis => ECO:0000250 |
Chain | Residue | Details |
A | LYS185 | |
B | LYS185 | |
C | LYS185 | |
D | LYS185 |