6ED7
Crystal structure of 7,8-diaminopelargonic acid synthase bound to inhibitor MAC13772
Functional Information from GO Data
| Chain | GOid | namespace | contents |
| A | 0004015 | molecular_function | adenosylmethionine-8-amino-7-oxononanoate transaminase activity |
| A | 0005737 | cellular_component | cytoplasm |
| A | 0008483 | molecular_function | transaminase activity |
| A | 0009102 | biological_process | biotin biosynthetic process |
| A | 0016740 | molecular_function | transferase activity |
| A | 0030170 | molecular_function | pyridoxal phosphate binding |
| A | 0042803 | molecular_function | protein homodimerization activity |
| B | 0004015 | molecular_function | adenosylmethionine-8-amino-7-oxononanoate transaminase activity |
| B | 0005737 | cellular_component | cytoplasm |
| B | 0008483 | molecular_function | transaminase activity |
| B | 0009102 | biological_process | biotin biosynthetic process |
| B | 0016740 | molecular_function | transferase activity |
| B | 0030170 | molecular_function | pyridoxal phosphate binding |
| B | 0042803 | molecular_function | protein homodimerization activity |
| C | 0004015 | molecular_function | adenosylmethionine-8-amino-7-oxononanoate transaminase activity |
| C | 0005737 | cellular_component | cytoplasm |
| C | 0008483 | molecular_function | transaminase activity |
| C | 0009102 | biological_process | biotin biosynthetic process |
| C | 0016740 | molecular_function | transferase activity |
| C | 0030170 | molecular_function | pyridoxal phosphate binding |
| C | 0042803 | molecular_function | protein homodimerization activity |
| D | 0004015 | molecular_function | adenosylmethionine-8-amino-7-oxononanoate transaminase activity |
| D | 0005737 | cellular_component | cytoplasm |
| D | 0008483 | molecular_function | transaminase activity |
| D | 0009102 | biological_process | biotin biosynthetic process |
| D | 0016740 | molecular_function | transferase activity |
| D | 0030170 | molecular_function | pyridoxal phosphate binding |
| D | 0042803 | molecular_function | protein homodimerization activity |
| E | 0004015 | molecular_function | adenosylmethionine-8-amino-7-oxononanoate transaminase activity |
| E | 0005737 | cellular_component | cytoplasm |
| E | 0008483 | molecular_function | transaminase activity |
| E | 0009102 | biological_process | biotin biosynthetic process |
| E | 0016740 | molecular_function | transferase activity |
| E | 0030170 | molecular_function | pyridoxal phosphate binding |
| E | 0042803 | molecular_function | protein homodimerization activity |
| F | 0004015 | molecular_function | adenosylmethionine-8-amino-7-oxononanoate transaminase activity |
| F | 0005737 | cellular_component | cytoplasm |
| F | 0008483 | molecular_function | transaminase activity |
| F | 0009102 | biological_process | biotin biosynthetic process |
| F | 0016740 | molecular_function | transferase activity |
| F | 0030170 | molecular_function | pyridoxal phosphate binding |
| F | 0042803 | molecular_function | protein homodimerization activity |
| G | 0004015 | molecular_function | adenosylmethionine-8-amino-7-oxononanoate transaminase activity |
| G | 0005737 | cellular_component | cytoplasm |
| G | 0008483 | molecular_function | transaminase activity |
| G | 0009102 | biological_process | biotin biosynthetic process |
| G | 0016740 | molecular_function | transferase activity |
| G | 0030170 | molecular_function | pyridoxal phosphate binding |
| G | 0042803 | molecular_function | protein homodimerization activity |
| H | 0004015 | molecular_function | adenosylmethionine-8-amino-7-oxononanoate transaminase activity |
| H | 0005737 | cellular_component | cytoplasm |
| H | 0008483 | molecular_function | transaminase activity |
| H | 0009102 | biological_process | biotin biosynthetic process |
| H | 0016740 | molecular_function | transferase activity |
| H | 0030170 | molecular_function | pyridoxal phosphate binding |
| H | 0042803 | molecular_function | protein homodimerization activity |
Functional Information from PDB Data
| site_id | AC1 |
| Number of Residues | 10 |
| Details | binding site for residue J4J A 603 |
| Chain | Residue |
| A | TYR17 |
| B | GLY307 |
| A | TRP52 |
| A | TYR144 |
| A | ASP147 |
| A | ARG391 |
| A | PHE393 |
| A | J4J602 |
| A | HOH741 |
| B | GLY81 |
| site_id | AC2 |
| Number of Residues | 10 |
| Details | binding site for residue J4J B 603 |
| Chain | Residue |
| A | GLY307 |
| B | PRO16 |
| B | TYR17 |
| B | TRP52 |
| B | TYR144 |
| B | ASP147 |
| B | ARG391 |
| B | PHE393 |
| B | J4J602 |
| B | HOH749 |
| site_id | AC3 |
| Number of Residues | 10 |
| Details | binding site for residue J4J C 603 |
| Chain | Residue |
| C | PRO16 |
| C | TYR17 |
| C | TRP52 |
| C | TYR144 |
| C | ASP147 |
| C | ARG391 |
| C | PHE393 |
| C | J4J602 |
| C | HOH747 |
| D | GLY307 |
| site_id | AC4 |
| Number of Residues | 8 |
| Details | binding site for residue J4J D 603 |
| Chain | Residue |
| C | GLY307 |
| D | TYR17 |
| D | TYR144 |
| D | ASP147 |
| D | ARG391 |
| D | PHE393 |
| D | J4J602 |
| D | HOH761 |
| site_id | AC5 |
| Number of Residues | 10 |
| Details | binding site for residue J4J E 603 |
| Chain | Residue |
| E | TYR17 |
| E | TRP52 |
| E | TYR144 |
| E | ASP147 |
| E | ARG391 |
| E | PHE393 |
| E | J4J602 |
| E | HOH734 |
| F | GLY81 |
| F | GLY307 |
| site_id | AC6 |
| Number of Residues | 9 |
| Details | binding site for residue J4J F 603 |
| Chain | Residue |
| E | GLY307 |
| F | PRO16 |
| F | TYR17 |
| F | TRP52 |
| F | TYR144 |
| F | ASP147 |
| F | ARG391 |
| F | PHE393 |
| F | J4J602 |
| site_id | AC7 |
| Number of Residues | 10 |
| Details | binding site for residue J4J G 602 |
| Chain | Residue |
| G | PRO16 |
| G | TYR17 |
| G | TRP52 |
| G | TYR144 |
| G | ASP147 |
| G | ARG391 |
| G | PHE393 |
| G | J4J603 |
| H | GLY81 |
| H | GLY307 |
| site_id | AC8 |
| Number of Residues | 10 |
| Details | binding site for residue J4J H 603 |
| Chain | Residue |
| G | GLY81 |
| G | GLY307 |
| H | PRO16 |
| H | TYR17 |
| H | TRP52 |
| H | TYR144 |
| H | ASP147 |
| H | ARG391 |
| H | PHE393 |
| H | J4J602 |
| site_id | AC9 |
| Number of Residues | 21 |
| Details | binding site for residues PLP A 601 and J4J A 602 |
| Chain | Residue |
| A | TRP52 |
| A | GLY112 |
| A | SER113 |
| A | TYR144 |
| A | HIS145 |
| A | GLY146 |
| A | GLU211 |
| A | ALA217 |
| A | ASP245 |
| A | ILE247 |
| A | LYS274 |
| A | PHE393 |
| A | TYR398 |
| A | J4J603 |
| A | HOH701 |
| A | HOH737 |
| A | HOH744 |
| A | HOH785 |
| B | PRO308 |
| B | THR309 |
| B | HOH718 |
| site_id | AD1 |
| Number of Residues | 21 |
| Details | binding site for residues PLP B 601 and J4J B 602 |
| Chain | Residue |
| A | THR309 |
| A | HOH712 |
| B | TRP52 |
| B | GLY112 |
| B | SER113 |
| B | TYR144 |
| B | HIS145 |
| B | GLY146 |
| B | ALA217 |
| B | ASP245 |
| B | ILE247 |
| B | LYS274 |
| B | PHE393 |
| B | TYR398 |
| B | J4J603 |
| B | HOH709 |
| B | HOH711 |
| B | HOH714 |
| B | HOH767 |
| B | HOH779 |
| A | PRO308 |
| site_id | AD2 |
| Number of Residues | 19 |
| Details | binding site for residues PLP C 601 and J4J C 602 |
| Chain | Residue |
| C | TRP52 |
| C | GLY112 |
| C | SER113 |
| C | TYR144 |
| C | HIS145 |
| C | GLY146 |
| C | ALA217 |
| C | ASP245 |
| C | ILE247 |
| C | LYS274 |
| C | PHE393 |
| C | TYR398 |
| C | J4J603 |
| C | HOH710 |
| C | HOH727 |
| C | HOH733 |
| D | PRO308 |
| D | THR309 |
| D | HOH730 |
| site_id | AD3 |
| Number of Residues | 23 |
| Details | binding site for residues PLP D 601 and J4J D 602 |
| Chain | Residue |
| C | PRO308 |
| C | THR309 |
| C | HOH736 |
| D | TRP52 |
| D | GLY112 |
| D | SER113 |
| D | TYR144 |
| D | HIS145 |
| D | GLY146 |
| D | ALA217 |
| D | ASP245 |
| D | ILE247 |
| D | ALA248 |
| D | LYS274 |
| D | PHE393 |
| D | TYR398 |
| D | J4J603 |
| D | HOH701 |
| D | HOH728 |
| D | HOH734 |
| D | HOH738 |
| D | HOH744 |
| D | HOH752 |
| site_id | AD4 |
| Number of Residues | 20 |
| Details | binding site for residues PLP E 601 and J4J E 602 |
| Chain | Residue |
| E | TRP52 |
| E | SER111 |
| E | GLY112 |
| E | SER113 |
| E | TYR144 |
| E | HIS145 |
| E | GLU211 |
| E | ALA217 |
| E | ASP245 |
| E | ILE247 |
| E | LYS274 |
| E | PHE393 |
| E | TYR398 |
| E | J4J603 |
| E | HOH729 |
| E | HOH754 |
| E | HOH759 |
| E | HOH773 |
| F | PRO308 |
| F | THR309 |
| site_id | AD5 |
| Number of Residues | 22 |
| Details | binding site for residues PLP F 601 and J4J F 602 |
| Chain | Residue |
| E | PRO308 |
| E | THR309 |
| E | HOH730 |
| F | TRP52 |
| F | GLY112 |
| F | SER113 |
| F | TYR144 |
| F | HIS145 |
| F | GLY146 |
| F | ALA217 |
| F | ASP245 |
| F | ILE247 |
| F | LYS274 |
| F | PHE393 |
| F | TYR398 |
| F | J4J603 |
| F | HOH742 |
| F | HOH743 |
| F | HOH746 |
| F | HOH755 |
| F | HOH756 |
| F | HOH769 |
| site_id | AD6 |
| Number of Residues | 22 |
| Details | binding site for residues PLP G 601 and J4J G 603 |
| Chain | Residue |
| G | TRP52 |
| G | TRP53 |
| G | GLY112 |
| G | SER113 |
| G | TYR144 |
| G | HIS145 |
| G | GLY146 |
| G | ALA217 |
| G | ASP245 |
| G | ILE247 |
| G | ALA248 |
| G | LYS274 |
| G | PHE393 |
| G | TYR398 |
| G | J4J602 |
| G | HOH706 |
| G | HOH723 |
| G | HOH737 |
| G | HOH740 |
| H | PRO308 |
| H | THR309 |
| H | HOH738 |
| site_id | AD7 |
| Number of Residues | 22 |
| Details | binding site for residues PLP H 601 and J4J H 602 |
| Chain | Residue |
| G | PRO308 |
| G | THR309 |
| H | TRP52 |
| H | GLY112 |
| H | SER113 |
| H | TYR144 |
| H | HIS145 |
| H | GLY146 |
| H | GLU211 |
| H | ALA217 |
| H | ASP245 |
| H | ILE247 |
| H | ALA248 |
| H | LYS274 |
| H | PHE393 |
| H | TYR398 |
| H | J4J603 |
| H | HOH710 |
| H | HOH723 |
| H | HOH734 |
| H | HOH736 |
| H | HOH761 |
Functional Information from PROSITE/UniProt
| site_id | PS00600 |
| Number of Residues | 38 |
| Details | AA_TRANSFER_CLASS_3 Aminotransferases class-III pyridoxal-phosphate attachment site. LIaDEIat.GFgRtGklfacehaeiap....DILclGKaltGG |
| Chain | Residue | Details |
| A | LEU242-GLY279 |
Functional Information from SwissProt/UniProt
| site_id | SWS_FT_FI1 |
| Number of Residues | 16 |
| Details | Binding site: {"evidences":[{"source":"PubMed","id":"10452893","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"12218056","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"1MLY","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1QJ3","evidenceCode":"ECO:0007744"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI2 |
| Number of Residues | 16 |
| Details | Binding site: {"evidences":[{"source":"PubMed","id":"10452893","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"12379100","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"14756557","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"1DTY","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1MGV","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1QJ3","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1QJ5","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1S07","evidenceCode":"ECO:0007744"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI3 |
| Number of Residues | 8 |
| Details | Binding site: {"evidences":[{"source":"PubMed","id":"10452893","evidenceCode":"ECO:0000305"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI4 |
| Number of Residues | 8 |
| Details | Binding site: {"evidences":[{"source":"PubMed","id":"10452893","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"12379100","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"14756557","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"1MGV","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1QJ3","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1QJ5","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1S07","evidenceCode":"ECO:0007744"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI5 |
| Number of Residues | 8 |
| Details | Binding site: {"evidences":[{"source":"PubMed","id":"10452893","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"1QJ3","evidenceCode":"ECO:0007744"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI6 |
| Number of Residues | 8 |
| Details | Binding site: {"evidences":[{"source":"PubMed","id":"10452893","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"12218056","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"1MLY","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1MLZ","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1QJ3","evidenceCode":"ECO:0007744"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI7 |
| Number of Residues | 8 |
| Details | Site: {"description":"Participates in the substrate recognition with KAPA and in a stacking interaction with the adenine ring of SAM","evidences":[{"evidenceCode":"ECO:0000305"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI8 |
| Number of Residues | 8 |
| Details | Modified residue: {"description":"N6-(pyridoxal phosphate)lysine","evidences":[{"source":"PubMed","id":"12379100","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"14756557","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"1DTY","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1MGV","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1QJ3","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1QJ5","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1S06","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1S08","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1S09","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1S0A","evidenceCode":"ECO:0007744"}]} |
| Chain | Residue | Details |
Catalytic Information from CSA
| site_id | MCSA1 |
| Number of Residues | 4 |
| Details | M-CSA 249 |
| Chain | Residue | Details |
| A | TYR17 | electrostatic stabiliser, hydrogen bond acceptor, hydrogen bond donor, steric role |
| A | TYR144 | hydrogen bond acceptor, steric role, van der waals interaction |
| A | ASP245 | electrostatic stabiliser, hydrogen bond acceptor, increase basicity, steric role |
| A | LYS274 | covalently attached, electron pair acceptor, electron pair donor, hydrogen bond acceptor, hydrogen bond donor, nucleofuge, nucleophile, proton acceptor, proton donor |
| site_id | MCSA2 |
| Number of Residues | 4 |
| Details | M-CSA 249 |
| Chain | Residue | Details |
| B | TYR17 | electrostatic stabiliser, hydrogen bond acceptor, hydrogen bond donor, steric role |
| B | TYR144 | hydrogen bond acceptor, steric role, van der waals interaction |
| B | ASP245 | electrostatic stabiliser, hydrogen bond acceptor, increase basicity, steric role |
| B | LYS274 | covalently attached, electron pair acceptor, electron pair donor, hydrogen bond acceptor, hydrogen bond donor, nucleofuge, nucleophile, proton acceptor, proton donor |
| site_id | MCSA3 |
| Number of Residues | 4 |
| Details | M-CSA 249 |
| Chain | Residue | Details |
| C | TYR17 | electrostatic stabiliser, hydrogen bond acceptor, hydrogen bond donor, steric role |
| C | TYR144 | hydrogen bond acceptor, steric role, van der waals interaction |
| C | ASP245 | electrostatic stabiliser, hydrogen bond acceptor, increase basicity, steric role |
| C | LYS274 | covalently attached, electron pair acceptor, electron pair donor, hydrogen bond acceptor, hydrogen bond donor, nucleofuge, nucleophile, proton acceptor, proton donor |
| site_id | MCSA4 |
| Number of Residues | 4 |
| Details | M-CSA 249 |
| Chain | Residue | Details |
| D | TYR17 | electrostatic stabiliser, hydrogen bond acceptor, hydrogen bond donor, steric role |
| D | TYR144 | hydrogen bond acceptor, steric role, van der waals interaction |
| D | ASP245 | electrostatic stabiliser, hydrogen bond acceptor, increase basicity, steric role |
| D | LYS274 | covalently attached, electron pair acceptor, electron pair donor, hydrogen bond acceptor, hydrogen bond donor, nucleofuge, nucleophile, proton acceptor, proton donor |
| site_id | MCSA5 |
| Number of Residues | 4 |
| Details | M-CSA 249 |
| Chain | Residue | Details |
| E | TYR17 | electrostatic stabiliser, hydrogen bond acceptor, hydrogen bond donor, steric role |
| E | TYR144 | hydrogen bond acceptor, steric role, van der waals interaction |
| E | ASP245 | electrostatic stabiliser, hydrogen bond acceptor, increase basicity, steric role |
| E | LYS274 | covalently attached, electron pair acceptor, electron pair donor, hydrogen bond acceptor, hydrogen bond donor, nucleofuge, nucleophile, proton acceptor, proton donor |
| site_id | MCSA6 |
| Number of Residues | 4 |
| Details | M-CSA 249 |
| Chain | Residue | Details |
| F | TYR17 | electrostatic stabiliser, hydrogen bond acceptor, hydrogen bond donor, steric role |
| F | TYR144 | hydrogen bond acceptor, steric role, van der waals interaction |
| F | ASP245 | electrostatic stabiliser, hydrogen bond acceptor, increase basicity, steric role |
| F | LYS274 | covalently attached, electron pair acceptor, electron pair donor, hydrogen bond acceptor, hydrogen bond donor, nucleofuge, nucleophile, proton acceptor, proton donor |
| site_id | MCSA7 |
| Number of Residues | 4 |
| Details | M-CSA 249 |
| Chain | Residue | Details |
| G | TYR17 | electrostatic stabiliser, hydrogen bond acceptor, hydrogen bond donor, steric role |
| G | TYR144 | hydrogen bond acceptor, steric role, van der waals interaction |
| G | ASP245 | electrostatic stabiliser, hydrogen bond acceptor, increase basicity, steric role |
| G | LYS274 | covalently attached, electron pair acceptor, electron pair donor, hydrogen bond acceptor, hydrogen bond donor, nucleofuge, nucleophile, proton acceptor, proton donor |
| site_id | MCSA8 |
| Number of Residues | 4 |
| Details | M-CSA 249 |
| Chain | Residue | Details |
| H | TYR17 | electrostatic stabiliser, hydrogen bond acceptor, hydrogen bond donor, steric role |
| H | TYR144 | hydrogen bond acceptor, steric role, van der waals interaction |
| H | ASP245 | electrostatic stabiliser, hydrogen bond acceptor, increase basicity, steric role |
| H | LYS274 | covalently attached, electron pair acceptor, electron pair donor, hydrogen bond acceptor, hydrogen bond donor, nucleofuge, nucleophile, proton acceptor, proton donor |
