2PDA
CRYSTAL STRUCTURE OF THE COMPLEX BETWEEN PYRUVATE-FERREDOXIN OXIDOREDUCTASE FROM DESULFOVIBRIO AFRICANUS AND PYRUVATE.
Functional Information from GO Data
| Chain | GOid | namespace | contents |
| A | 0003824 | molecular_function | catalytic activity |
| A | 0005506 | molecular_function | iron ion binding |
| A | 0005737 | cellular_component | cytoplasm |
| A | 0006086 | biological_process | acetyl-CoA biosynthetic process from pyruvate |
| A | 0006979 | biological_process | response to oxidative stress |
| A | 0016491 | molecular_function | oxidoreductase activity |
| A | 0016903 | molecular_function | oxidoreductase activity, acting on the aldehyde or oxo group of donors |
| A | 0019164 | molecular_function | pyruvate synthase activity |
| A | 0022900 | biological_process | electron transport chain |
| A | 0030976 | molecular_function | thiamine pyrophosphate binding |
| A | 0046872 | molecular_function | metal ion binding |
| A | 0051536 | molecular_function | iron-sulfur cluster binding |
| A | 0051539 | molecular_function | 4 iron, 4 sulfur cluster binding |
| B | 0003824 | molecular_function | catalytic activity |
| B | 0005506 | molecular_function | iron ion binding |
| B | 0005737 | cellular_component | cytoplasm |
| B | 0006086 | biological_process | acetyl-CoA biosynthetic process from pyruvate |
| B | 0006979 | biological_process | response to oxidative stress |
| B | 0016491 | molecular_function | oxidoreductase activity |
| B | 0016903 | molecular_function | oxidoreductase activity, acting on the aldehyde or oxo group of donors |
| B | 0019164 | molecular_function | pyruvate synthase activity |
| B | 0022900 | biological_process | electron transport chain |
| B | 0030976 | molecular_function | thiamine pyrophosphate binding |
| B | 0046872 | molecular_function | metal ion binding |
| B | 0051536 | molecular_function | iron-sulfur cluster binding |
| B | 0051539 | molecular_function | 4 iron, 4 sulfur cluster binding |
Functional Information from PDB Data
| site_id | AC1 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE MG A 1237 |
| Chain | Residue |
| A | THR991 |
| A | VAL993 |
| A | TPP1236 |
| A | HOH2004 |
| A | ASP963 |
| site_id | AC2 |
| Number of Residues | 7 |
| Details | BINDING SITE FOR RESIDUE CA A 1238 |
| Chain | Residue |
| A | ASP983 |
| A | ASN985 |
| A | ALA1056 |
| A | GLU1057 |
| A | PHE1059 |
| A | GLY1061 |
| A | SER1063 |
| site_id | AC3 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE MG B 1244 |
| Chain | Residue |
| B | ASP963 |
| B | THR991 |
| B | VAL993 |
| B | TPP1243 |
| B | HOH2104 |
| site_id | AC4 |
| Number of Residues | 7 |
| Details | BINDING SITE FOR RESIDUE CA B 1245 |
| Chain | Residue |
| B | ASP983 |
| B | ASN985 |
| B | ALA1056 |
| B | GLU1057 |
| B | PHE1059 |
| B | GLY1061 |
| B | SER1063 |
| site_id | AC5 |
| Number of Residues | 10 |
| Details | BINDING SITE FOR RESIDUE SF4 A 1233 |
| Chain | Residue |
| A | TRP684 |
| A | CYS689 |
| A | ILE690 |
| A | CYS692 |
| A | ASN693 |
| A | CYS695 |
| A | CYS755 |
| A | PRO756 |
| A | ALA761 |
| A | LEU762 |
| site_id | AC6 |
| Number of Residues | 10 |
| Details | BINDING SITE FOR RESIDUE SF4 A 1234 |
| Chain | Residue |
| A | PRO682 |
| A | CYS699 |
| A | ALA703 |
| A | ILE704 |
| A | CYS745 |
| A | MET746 |
| A | GLY747 |
| A | CYS748 |
| A | GLY749 |
| A | CYS751 |
| site_id | AC7 |
| Number of Residues | 7 |
| Details | BINDING SITE FOR RESIDUE SF4 A 1235 |
| Chain | Residue |
| A | LYS459 |
| A | CYS812 |
| A | CYS815 |
| A | GLU817 |
| A | CYS840 |
| A | CYS1071 |
| A | ILE1072 |
| site_id | AC8 |
| Number of Residues | 22 |
| Details | BINDING SITE FOR RESIDUE TPP A 1236 |
| Chain | Residue |
| A | PRO29 |
| A | GLU64 |
| A | GLU817 |
| A | GLY839 |
| A | CYS840 |
| A | PHE869 |
| A | GLU870 |
| A | GLY962 |
| A | ASP963 |
| A | GLY964 |
| A | TRP965 |
| A | THR991 |
| A | VAL993 |
| A | TYR994 |
| A | SER995 |
| A | ASN996 |
| A | THR997 |
| A | MG1237 |
| A | PYR1239 |
| A | HOH2001 |
| A | HOH2003 |
| A | HOH2004 |
| site_id | AC9 |
| Number of Residues | 7 |
| Details | BINDING SITE FOR RESIDUE PYR A 1239 |
| Chain | Residue |
| A | ILE30 |
| A | THR31 |
| A | ARG114 |
| A | ASN996 |
| A | THR997 |
| A | TPP1236 |
| B | MET1202 |
| site_id | BC1 |
| Number of Residues | 10 |
| Details | BINDING SITE FOR RESIDUE SF4 B 1240 |
| Chain | Residue |
| B | TRP684 |
| B | CYS689 |
| B | ILE690 |
| B | CYS692 |
| B | ASN693 |
| B | CYS695 |
| B | CYS755 |
| B | PRO756 |
| B | ALA761 |
| B | LEU762 |
| site_id | BC2 |
| Number of Residues | 10 |
| Details | BINDING SITE FOR RESIDUE SF4 B 1241 |
| Chain | Residue |
| B | CYS699 |
| B | ALA703 |
| B | ILE704 |
| B | CYS745 |
| B | MET746 |
| B | GLY747 |
| B | CYS748 |
| B | GLY749 |
| B | CYS751 |
| B | PRO682 |
| site_id | BC3 |
| Number of Residues | 8 |
| Details | BINDING SITE FOR RESIDUE SF4 B 1242 |
| Chain | Residue |
| A | MET1203 |
| B | LYS459 |
| B | CYS812 |
| B | CYS815 |
| B | GLU817 |
| B | CYS840 |
| B | CYS1071 |
| B | ILE1072 |
| site_id | BC4 |
| Number of Residues | 22 |
| Details | BINDING SITE FOR RESIDUE TPP B 1243 |
| Chain | Residue |
| B | PRO29 |
| B | GLU64 |
| B | GLU817 |
| B | GLY839 |
| B | CYS840 |
| B | PHE869 |
| B | GLU870 |
| B | GLY962 |
| B | ASP963 |
| B | GLY964 |
| B | TRP965 |
| B | THR991 |
| B | VAL993 |
| B | TYR994 |
| B | SER995 |
| B | ASN996 |
| B | THR997 |
| B | MG1244 |
| B | PYR1246 |
| B | HOH2101 |
| B | HOH2103 |
| B | HOH2104 |
| site_id | BC5 |
| Number of Residues | 7 |
| Details | BINDING SITE FOR RESIDUE PYR B 1246 |
| Chain | Residue |
| A | MET1202 |
| B | ILE30 |
| B | THR31 |
| B | ARG114 |
| B | ASN996 |
| B | THR997 |
| B | TPP1243 |
| site_id | MGA |
| Number of Residues | 4 |
| Details | MG BINDING SITE |
| Chain | Residue |
| A | ASP963 |
| A | THR991 |
| A | VAL993 |
| A | TPP1236 |
| site_id | MGB |
| Number of Residues | 4 |
| Details | MG BINDING SITE |
| Chain | Residue |
| B | ASP963 |
| B | THR991 |
| B | VAL993 |
| B | TPP1243 |
Functional Information from PROSITE/UniProt
| site_id | PS00198 |
| Number of Residues | 12 |
| Details | 4FE4S_FER_1 4Fe-4S ferredoxin-type iron-sulfur binding region signature. CiQCNqCAfVCP |
| Chain | Residue | Details |
| A | CYS689-PRO700 | |
| A | CYS745-PRO756 |
Functional Information from SwissProt/UniProt
| site_id | SWS_FT_FI1 |
| Number of Residues | 4 |
| Details | BINDING: BINDING => ECO:0000269|PubMed:10048931, ECO:0000269|PubMed:16472741 |
| Chain | Residue | Details |
| A | THR31 | |
| A | ARG114 | |
| B | THR31 | |
| B | ARG114 |
| site_id | SWS_FT_FI2 |
| Number of Residues | 4 |
| Details | BINDING: BINDING => ECO:0000269|PubMed:10048931, ECO:0000269|PubMed:11752578 |
| Chain | Residue | Details |
| A | GLU64 | |
| A | CYS1071 | |
| B | GLU64 | |
| B | CYS1071 |
| site_id | SWS_FT_FI3 |
| Number of Residues | 8 |
| Details | BINDING: BINDING => ECO:0000250|UniProtKB:Q2RMD6 |
| Chain | Residue | Details |
| A | ALA427 | |
| A | LYS459 | |
| A | ASN560 | |
| A | ASN602 | |
| B | ALA427 | |
| B | LYS459 | |
| B | ASN560 | |
| B | ASN602 |
| site_id | SWS_FT_FI4 |
| Number of Residues | 44 |
| Details | BINDING: BINDING => ECO:0000269|PubMed:10048931, ECO:0000269|PubMed:11752578, ECO:0000269|PubMed:16472741 |
| Chain | Residue | Details |
| A | CYS689 | |
| A | CYS815 | |
| A | GLU817 | |
| A | CYS840 | |
| A | GLY962 | |
| A | ASP963 | |
| A | ASP983 | |
| A | ASN985 | |
| A | THR991 | |
| A | VAL993 | |
| A | ALA1056 | |
| A | CYS692 | |
| A | PHE1059 | |
| A | GLY1061 | |
| A | SER1063 | |
| B | CYS689 | |
| B | CYS692 | |
| B | CYS695 | |
| B | CYS699 | |
| B | CYS745 | |
| B | CYS748 | |
| B | CYS751 | |
| A | CYS695 | |
| B | CYS755 | |
| B | CYS812 | |
| B | CYS815 | |
| B | GLU817 | |
| B | CYS840 | |
| B | GLY962 | |
| B | ASP963 | |
| B | ASP983 | |
| B | ASN985 | |
| B | THR991 | |
| A | CYS699 | |
| B | VAL993 | |
| B | ALA1056 | |
| B | PHE1059 | |
| B | GLY1061 | |
| B | SER1063 | |
| A | CYS745 | |
| A | CYS748 | |
| A | CYS751 | |
| A | CYS755 | |
| A | CYS812 |
| site_id | SWS_FT_FI5 |
| Number of Residues | 8 |
| Details | SITE: Important for catalytic activity => ECO:0000303|PubMed:10048931 |
| Chain | Residue | Details |
| A | THR31 | |
| A | GLU64 | |
| A | ARG114 | |
| A | ASN996 | |
| B | THR31 | |
| B | GLU64 | |
| B | ARG114 | |
| B | ASN996 |
Catalytic Information from CSA
| site_id | MCSA1 |
| Number of Residues | 4 |
| Details | M-CSA 119 |
| Chain | Residue | Details |
| A | THR31 | electrostatic stabiliser, hydrogen bond donor |
| A | GLU64 | hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor |
| A | ARG114 | electrostatic stabiliser, hydrogen bond donor |
| A | ASN996 | electrostatic stabiliser, hydrogen bond donor |
| site_id | MCSA2 |
| Number of Residues | 4 |
| Details | M-CSA 119 |
| Chain | Residue | Details |
| B | THR31 | electrostatic stabiliser, hydrogen bond donor |
| B | GLU64 | hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor |
| B | ARG114 | electrostatic stabiliser, hydrogen bond donor |
| B | ASN996 | electrostatic stabiliser, hydrogen bond donor |
