3QXX
Crystal structure of dethiobiotin synthetase (BioD) from Helicobacter pylori complexed with GDP and 8-aminocaprylic acid
Functional Information from GO Data
| Chain | GOid | namespace | contents |
| A | 0000166 | molecular_function | nucleotide binding |
| A | 0000287 | molecular_function | magnesium ion binding |
| A | 0004141 | molecular_function | dethiobiotin synthase activity |
| A | 0005524 | molecular_function | ATP binding |
| A | 0005737 | cellular_component | cytoplasm |
| A | 0005829 | cellular_component | cytosol |
| A | 0009102 | biological_process | biotin biosynthetic process |
| A | 0016874 | molecular_function | ligase activity |
| A | 0046872 | molecular_function | metal ion binding |
Functional Information from PDB Data
| site_id | AC1 |
| Number of Residues | 13 |
| Details | BINDING SITE FOR RESIDUE 8AC A 221 |
| Chain | Residue |
| A | THR9 |
| A | HOH252 |
| A | HOH291 |
| A | HOH293 |
| A | HOH377 |
| A | THR39 |
| A | SER79 |
| A | VAL123 |
| A | GLY151 |
| A | LEU152 |
| A | ILE153 |
| A | ASN154 |
| A | PO4225 |
| site_id | AC2 |
| Number of Residues | 20 |
| Details | BINDING SITE FOR RESIDUE GDP A 222 |
| Chain | Residue |
| A | ASN10 |
| A | ALA11 |
| A | GLY12 |
| A | LYS13 |
| A | THR14 |
| A | THR15 |
| A | GLU116 |
| A | ASN175 |
| A | LYS177 |
| A | GLY178 |
| A | MG223 |
| A | MG224 |
| A | PO4225 |
| A | HOH261 |
| A | HOH269 |
| A | HOH290 |
| A | HOH303 |
| A | HOH413 |
| A | HOH517 |
| A | HOH534 |
| site_id | AC3 |
| Number of Residues | 7 |
| Details | BINDING SITE FOR RESIDUE MG A 223 |
| Chain | Residue |
| A | GDP222 |
| A | MG224 |
| A | PO4225 |
| A | HOH269 |
| A | HOH289 |
| A | HOH290 |
| A | HOH517 |
| site_id | AC4 |
| Number of Residues | 8 |
| Details | BINDING SITE FOR RESIDUE MG A 224 |
| Chain | Residue |
| A | THR14 |
| A | LYS35 |
| A | ASP50 |
| A | GLU116 |
| A | GDP222 |
| A | MG223 |
| A | PO4225 |
| A | HOH517 |
| site_id | AC5 |
| Number of Residues | 15 |
| Details | BINDING SITE FOR RESIDUE PO4 A 225 |
| Chain | Residue |
| A | THR9 |
| A | LYS13 |
| A | LYS35 |
| A | ASP50 |
| A | GLU116 |
| A | ALA118 |
| A | GLY119 |
| A | 8AC221 |
| A | GDP222 |
| A | MG223 |
| A | MG224 |
| A | HOH255 |
| A | HOH289 |
| A | HOH290 |
| A | HOH493 |
| site_id | AC6 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE EDO A 226 |
| Chain | Residue |
| A | ASN42 |
| A | ASP43 |
| A | ARG74 |
| A | HIS76 |
| site_id | AC7 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE EDO A 227 |
| Chain | Residue |
| A | HIS0 |
| A | MET1 |
| A | LYS139 |
| A | LYS141 |
| A | SER220 |
| site_id | AC8 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE EDO A 228 |
| Chain | Residue |
| A | LYS171 |
| A | ASN200 |
| A | PRO201 |
| A | HOH474 |
| A | HOH511 |
| site_id | AC9 |
| Number of Residues | 7 |
| Details | BINDING SITE FOR RESIDUE EDO A 229 |
| Chain | Residue |
| A | PHE72 |
| A | TYR73 |
| A | ARG74 |
| A | TYR75 |
| A | ASP89 |
| A | HOH314 |
| A | HOH555 |
| site_id | BC1 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE EDO A 230 |
| Chain | Residue |
| A | GLN22 |
| A | ASP57 |
| A | HOH557 |
| site_id | BC2 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE EDO A 231 |
| Chain | Residue |
| A | TYR73 |
| A | ALA92 |
| A | PRO93 |
| site_id | BC3 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE GOL A 232 |
| Chain | Residue |
| A | ASN130 |
| A | ASP133 |
| A | HIS166 |
| A | HOH285 |
| A | HOH397 |
Functional Information from SwissProt/UniProt
| site_id | SWS_FT_FI1 |
| Number of Residues | 1 |
| Details | ACT_SITE: ACT_SITE => ECO:0000255|HAMAP-Rule:MF_00336, ECO:0000305|PubMed:22284390 |
| Chain | Residue | Details |
| A | LYS35 |
| site_id | SWS_FT_FI2 |
| Number of Residues | 1 |
| Details | BINDING: BINDING => ECO:0000255|HAMAP-Rule:MF_00336, ECO:0000269|PubMed:22284390, ECO:0007744|PDB:3MLE, ECO:0007744|PDB:3QXC, ECO:0007744|PDB:3QXH, ECO:0007744|PDB:3QXJ, ECO:0007744|PDB:3QXS |
| Chain | Residue | Details |
| A | THR9 |
| site_id | SWS_FT_FI3 |
| Number of Residues | 2 |
| Details | BINDING: BINDING => ECO:0000255|HAMAP-Rule:MF_00336, ECO:0000269|PubMed:22284390, ECO:0007744|PDB:3MLE, ECO:0007744|PDB:3QXC, ECO:0007744|PDB:3QXH, ECO:0007744|PDB:3QXJ, ECO:0007744|PDB:3QXS, ECO:0007744|PDB:3QXX, ECO:0007744|PDB:3QY0 |
| Chain | Residue | Details |
| A | THR14 | |
| A | GLU116 |
| site_id | SWS_FT_FI4 |
| Number of Residues | 1 |
| Details | BINDING: BINDING => ECO:0000269|PubMed:22284390, ECO:0007744|PDB:3MLE, ECO:0007744|PDB:3QXH, ECO:0007744|PDB:3QXX, ECO:0007744|PDB:3QY0 |
| Chain | Residue | Details |
| A | LYS35 |
| site_id | SWS_FT_FI5 |
| Number of Residues | 1 |
| Details | BINDING: BINDING => ECO:0000255|HAMAP-Rule:MF_00336, ECO:0000269|PubMed:22284390 |
| Chain | Residue | Details |
| A | THR39 |
| site_id | SWS_FT_FI6 |
| Number of Residues | 1 |
| Details | BINDING: BINDING => ECO:0000269|PubMed:22284390, ECO:0007744|PDB:3MLE, ECO:0007744|PDB:3QXC, ECO:0007744|PDB:3QXH, ECO:0007744|PDB:3QXJ, ECO:0007744|PDB:3QXS, ECO:0007744|PDB:3QXX, ECO:0007744|PDB:3QY0 |
| Chain | Residue | Details |
| A | ASP50 |
| site_id | SWS_FT_FI7 |
| Number of Residues | 1 |
| Details | BINDING: BINDING => ECO:0000269|PubMed:22284390, ECO:0007744|PDB:3MLE |
| Chain | Residue | Details |
| A | GLY151 |
| site_id | SWS_FT_FI8 |
| Number of Residues | 1 |
| Details | BINDING: BINDING => ECO:0000269|PubMed:22284390, ECO:0007744|PDB:3QXC, ECO:0007744|PDB:3QXS |
| Chain | Residue | Details |
| A | ASN175 |
