3FLK
Crystal Structure of Tartrate Dehydrogenase from Pseudomonas putida in complex with NADH, oxalate and metal ion
Functional Information from GO Data
Chain | GOid | namespace | contents |
A | 0000287 | molecular_function | magnesium ion binding |
A | 0005737 | cellular_component | cytoplasm |
A | 0009027 | molecular_function | tartrate dehydrogenase activity |
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 | 0016829 | molecular_function | lyase activity |
A | 0046553 | molecular_function | D-malate dehydrogenase (decarboxylating) (NAD+) activity |
A | 0046872 | molecular_function | metal ion binding |
A | 0050319 | molecular_function | tartrate decarboxylase activity |
A | 0051287 | molecular_function | NAD binding |
B | 0000287 | molecular_function | magnesium ion binding |
B | 0005737 | cellular_component | cytoplasm |
B | 0009027 | molecular_function | tartrate dehydrogenase activity |
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 | 0016829 | molecular_function | lyase activity |
B | 0046553 | molecular_function | D-malate dehydrogenase (decarboxylating) (NAD+) activity |
B | 0046872 | molecular_function | metal ion binding |
B | 0050319 | molecular_function | tartrate decarboxylase activity |
B | 0051287 | molecular_function | NAD binding |
C | 0000287 | molecular_function | magnesium ion binding |
C | 0005737 | cellular_component | cytoplasm |
C | 0009027 | molecular_function | tartrate dehydrogenase activity |
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 | 0016829 | molecular_function | lyase activity |
C | 0046553 | molecular_function | D-malate dehydrogenase (decarboxylating) (NAD+) activity |
C | 0046872 | molecular_function | metal ion binding |
C | 0050319 | molecular_function | tartrate decarboxylase activity |
C | 0051287 | molecular_function | NAD binding |
D | 0000287 | molecular_function | magnesium ion binding |
D | 0005737 | cellular_component | cytoplasm |
D | 0009027 | molecular_function | tartrate dehydrogenase activity |
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 | 0016829 | molecular_function | lyase activity |
D | 0046553 | molecular_function | D-malate dehydrogenase (decarboxylating) (NAD+) activity |
D | 0046872 | molecular_function | metal ion binding |
D | 0050319 | molecular_function | tartrate decarboxylase activity |
D | 0051287 | molecular_function | NAD binding |
Functional Information from PDB Data
site_id | AC1 |
Number of Residues | 5 |
Details | BINDING SITE FOR RESIDUE MG A 401 |
Chain | Residue |
A | ASP250 |
A | OXL403 |
A | HOH665 |
A | HOH666 |
B | ASP225 |
site_id | AC2 |
Number of Residues | 33 |
Details | BINDING SITE FOR RESIDUE NAI A 402 |
Chain | Residue |
A | GLY79 |
A | PRO81 |
A | ASP86 |
A | LEU94 |
A | ILE263 |
A | GLU282 |
A | HIS285 |
A | GLY286 |
A | SER287 |
A | ALA288 |
A | ILE291 |
A | ASN298 |
A | OXL403 |
A | NH4404 |
A | HOH505 |
A | HOH517 |
A | HOH520 |
A | HOH531 |
A | HOH548 |
A | HOH619 |
A | HOH631 |
A | HOH667 |
A | HOH668 |
A | HOH669 |
A | HOH671 |
B | ASN194 |
B | HIS223 |
B | ILE226 |
B | ARG230 |
A | ILE16 |
A | PHE75 |
A | ALA77 |
A | VAL78 |
site_id | AC3 |
Number of Residues | 9 |
Details | BINDING SITE FOR RESIDUE OXL A 403 |
Chain | Residue |
A | ARG98 |
A | ARG108 |
A | ARG134 |
A | ASP250 |
A | MG401 |
A | NAI402 |
A | HOH600 |
B | LYS192 |
B | ASP225 |
site_id | AC4 |
Number of Residues | 5 |
Details | BINDING SITE FOR RESIDUE NH4 A 404 |
Chain | Residue |
A | GLY76 |
A | GLU282 |
A | PRO283 |
A | HIS285 |
A | NAI402 |
site_id | AC5 |
Number of Residues | 5 |
Details | BINDING SITE FOR RESIDUE MG A 405 |
Chain | Residue |
A | ASP225 |
B | ASP250 |
B | OXL402 |
B | HOH659 |
B | HOH660 |
site_id | AC6 |
Number of Residues | 6 |
Details | BINDING SITE FOR RESIDUE SO4 A 406 |
Chain | Residue |
A | ARG111 |
A | TRP304 |
A | LEU308 |
A | HIS324 |
A | LEU328 |
A | HOH721 |
site_id | AC7 |
Number of Residues | 3 |
Details | BINDING SITE FOR RESIDUE SO4 A 407 |
Chain | Residue |
A | GLN234 |
A | ARG237 |
C | ARG7 |
site_id | AC8 |
Number of Residues | 5 |
Details | BINDING SITE FOR RESIDUE SO4 A 408 |
Chain | Residue |
A | LYS57 |
A | PRO60 |
A | ASP61 |
A | ASP62 |
A | HOH693 |
site_id | AC9 |
Number of Residues | 3 |
Details | BINDING SITE FOR RESIDUE SO4 A 409 |
Chain | Residue |
A | ARG182 |
A | GLU183 |
A | HOH547 |
site_id | BC1 |
Number of Residues | 33 |
Details | BINDING SITE FOR RESIDUE NAI B 401 |
Chain | Residue |
B | HOH562 |
B | HOH580 |
B | HOH620 |
B | HOH661 |
B | HOH665 |
B | HOH667 |
B | HOH669 |
B | HOH679 |
A | ASN194 |
A | HIS223 |
A | ILE226 |
A | ARG230 |
B | ILE16 |
B | ALA77 |
B | VAL78 |
B | GLY79 |
B | PRO81 |
B | ASP86 |
B | LEU94 |
B | ILE263 |
B | GLU282 |
B | HIS285 |
B | GLY286 |
B | SER287 |
B | ALA288 |
B | ASP290 |
B | ILE291 |
B | ALA297 |
B | ASN298 |
B | OXL402 |
B | NH4403 |
B | HOH509 |
B | HOH555 |
site_id | BC2 |
Number of Residues | 11 |
Details | BINDING SITE FOR RESIDUE OXL B 402 |
Chain | Residue |
A | LYS192 |
A | ASP225 |
A | MG405 |
B | ARG98 |
B | ARG108 |
B | ARG134 |
B | ASP250 |
B | NAI401 |
B | HOH659 |
B | HOH662 |
B | HOH702 |
site_id | BC3 |
Number of Residues | 5 |
Details | BINDING SITE FOR RESIDUE NH4 B 403 |
Chain | Residue |
B | GLY76 |
B | GLU282 |
B | PRO283 |
B | HIS285 |
B | NAI401 |
site_id | BC4 |
Number of Residues | 6 |
Details | BINDING SITE FOR RESIDUE SO4 B 404 |
Chain | Residue |
B | ARG111 |
B | TRP304 |
B | LEU308 |
B | HIS324 |
B | LEU328 |
B | HOH644 |
site_id | BC5 |
Number of Residues | 4 |
Details | BINDING SITE FOR RESIDUE SO4 B 405 |
Chain | Residue |
B | THR152 |
B | GLU153 |
B | PRO215 |
B | HOH673 |
site_id | BC6 |
Number of Residues | 3 |
Details | BINDING SITE FOR RESIDUE SO4 B 406 |
Chain | Residue |
B | GLN234 |
B | ARG237 |
D | ARG7 |
site_id | BC7 |
Number of Residues | 4 |
Details | BINDING SITE FOR RESIDUE DTT B 407 |
Chain | Residue |
B | ARG165 |
B | ARG206 |
B | HIS213 |
B | HOH538 |
site_id | BC8 |
Number of Residues | 6 |
Details | BINDING SITE FOR RESIDUE MG C 401 |
Chain | Residue |
C | ASP250 |
C | ASP254 |
C | OXL403 |
C | HOH521 |
C | HOH526 |
D | ASP225 |
site_id | BC9 |
Number of Residues | 30 |
Details | BINDING SITE FOR RESIDUE NAI C 402 |
Chain | Residue |
C | ILE16 |
C | ALA77 |
C | VAL78 |
C | GLY79 |
C | PRO81 |
C | ASP86 |
C | LEU94 |
C | GLU282 |
C | HIS285 |
C | GLY286 |
C | SER287 |
C | ALA288 |
C | ASP290 |
C | ILE291 |
C | ALA297 |
C | ASN298 |
C | OXL403 |
C | NH4404 |
C | HOH513 |
C | HOH532 |
C | HOH551 |
C | HOH574 |
C | HOH583 |
C | HOH588 |
C | HOH628 |
C | HOH677 |
D | ASN194 |
D | HIS223 |
D | ILE226 |
D | ARG230 |
site_id | CC1 |
Number of Residues | 9 |
Details | BINDING SITE FOR RESIDUE OXL C 403 |
Chain | Residue |
C | ARG98 |
C | ARG108 |
C | ARG134 |
C | ASP250 |
C | MG401 |
C | NAI402 |
C | HOH678 |
D | LYS192 |
D | ASP225 |
site_id | CC2 |
Number of Residues | 5 |
Details | BINDING SITE FOR RESIDUE NH4 C 404 |
Chain | Residue |
C | GLY76 |
C | GLU282 |
C | PRO283 |
C | HIS285 |
C | NAI402 |
site_id | CC3 |
Number of Residues | 5 |
Details | BINDING SITE FOR RESIDUE MG C 405 |
Chain | Residue |
C | ASP225 |
D | ASP250 |
D | OXL402 |
D | HOH705 |
D | HOH706 |
site_id | CC4 |
Number of Residues | 2 |
Details | BINDING SITE FOR RESIDUE SO4 C 406 |
Chain | Residue |
C | THR152 |
C | GLU153 |
site_id | CC5 |
Number of Residues | 3 |
Details | BINDING SITE FOR RESIDUE SO4 C 407 |
Chain | Residue |
C | LYS57 |
C | PRO60 |
C | ASP61 |
site_id | CC6 |
Number of Residues | 6 |
Details | BINDING SITE FOR RESIDUE SO4 C 408 |
Chain | Residue |
C | ARG111 |
C | TRP304 |
C | LEU308 |
C | HIS324 |
C | LEU328 |
C | HOH652 |
site_id | CC7 |
Number of Residues | 6 |
Details | BINDING SITE FOR RESIDUE DTT C 409 |
Chain | Residue |
C | ILE226 |
C | LEU233 |
C | GLN234 |
D | THR262 |
D | ILE263 |
D | HOH685 |
site_id | CC8 |
Number of Residues | 31 |
Details | BINDING SITE FOR RESIDUE NAI D 401 |
Chain | Residue |
C | ASN194 |
C | HIS223 |
C | ILE226 |
C | ARG230 |
C | HOH623 |
D | ILE16 |
D | ALA77 |
D | VAL78 |
D | GLY79 |
D | PRO81 |
D | ASP86 |
D | LEU94 |
D | ILE263 |
D | GLU282 |
D | HIS285 |
D | GLY286 |
D | SER287 |
D | ALA288 |
D | ASP290 |
D | ILE291 |
D | ALA297 |
D | ASN298 |
D | OXL402 |
D | NH4403 |
D | HOH512 |
D | HOH515 |
D | HOH534 |
D | HOH594 |
D | HOH654 |
D | HOH707 |
D | HOH708 |
site_id | CC9 |
Number of Residues | 10 |
Details | BINDING SITE FOR RESIDUE OXL D 402 |
Chain | Residue |
C | LYS192 |
C | ASP225 |
C | MG405 |
C | HOH535 |
D | ARG98 |
D | ARG108 |
D | ARG134 |
D | ASP250 |
D | NAI401 |
D | HOH764 |
site_id | DC1 |
Number of Residues | 5 |
Details | BINDING SITE FOR RESIDUE NH4 D 403 |
Chain | Residue |
D | GLY76 |
D | GLU282 |
D | PRO283 |
D | HIS285 |
D | NAI401 |
site_id | DC2 |
Number of Residues | 6 |
Details | BINDING SITE FOR RESIDUE SO4 D 404 |
Chain | Residue |
D | LYS57 |
D | PRO60 |
D | ASP61 |
D | ASP62 |
D | HOH671 |
D | HOH680 |
site_id | DC3 |
Number of Residues | 5 |
Details | BINDING SITE FOR RESIDUE SO4 D 405 |
Chain | Residue |
D | ARG26 |
D | SER358 |
D | HOH557 |
D | HOH642 |
D | HOH675 |
site_id | DC4 |
Number of Residues | 6 |
Details | BINDING SITE FOR RESIDUE SO4 D 406 |
Chain | Residue |
D | ARG111 |
D | TRP304 |
D | LEU308 |
D | HIS324 |
D | LEU328 |
D | HOH748 |
site_id | DC5 |
Number of Residues | 3 |
Details | BINDING SITE FOR RESIDUE SO4 D 407 |
Chain | Residue |
C | ARG165 |
D | ASN151 |
D | HOH711 |
site_id | DC6 |
Number of Residues | 7 |
Details | BINDING SITE FOR RESIDUE DTT D 408 |
Chain | Residue |
D | ASP14 |
D | GLY15 |
D | TRP80 |
D | PHE292 |
D | HOH632 |
D | HOH668 |
D | HOH738 |
Functional Information from PROSITE/UniProt
site_id | PS00470 |
Number of Residues | 20 |
Details | IDH_IMDH Isocitrate and isopropylmalate dehydrogenases signature. NLFGDIlSDlgPaca.GTIGI |
Chain | Residue | Details |
A | ASN246-ILE265 |
Functional Information from SwissProt/UniProt
site_id | SWS_FT_FI1 |
Number of Residues | 12 |
Details | BINDING: BINDING => ECO:0000250|UniProtKB:P37412 |
Chain | Residue | Details |
A | ASP225 | |
D | ASP225 | |
D | ILE251 | |
D | LEU255 | |
A | ILE251 | |
A | LEU255 | |
B | ASP225 | |
B | ILE251 | |
B | LEU255 | |
C | ASP225 | |
C | ILE251 | |
C | LEU255 |
Catalytic Information from CSA
site_id | CSA1 |
Number of Residues | 1 |
Details | Annotated By Reference To The Literature 1a05 |
Chain | Residue | Details |
A | TYR141 |
site_id | CSA2 |
Number of Residues | 1 |
Details | Annotated By Reference To The Literature 1a05 |
Chain | Residue | Details |
B | TYR141 |
site_id | CSA3 |
Number of Residues | 1 |
Details | Annotated By Reference To The Literature 1a05 |
Chain | Residue | Details |
C | TYR141 |
site_id | CSA4 |
Number of Residues | 1 |
Details | Annotated By Reference To The Literature 1a05 |
Chain | Residue | Details |
D | TYR141 |
site_id | CSA5 |
Number of Residues | 2 |
Details | Annotated By Reference To The Literature 1a05 |
Chain | Residue | Details |
A | LYS192 | |
A | ASP225 |
site_id | CSA6 |
Number of Residues | 2 |
Details | Annotated By Reference To The Literature 1a05 |
Chain | Residue | Details |
B | LYS192 | |
B | ASP225 |
site_id | CSA7 |
Number of Residues | 2 |
Details | Annotated By Reference To The Literature 1a05 |
Chain | Residue | Details |
C | LYS192 | |
C | ASP225 |
site_id | CSA8 |
Number of Residues | 2 |
Details | Annotated By Reference To The Literature 1a05 |
Chain | Residue | Details |
D | LYS192 | |
D | ASP225 |