1KJQ
Crystal structure of glycinamide ribonucleotide transformylase in complex with Mg-ADP
Functional Information from GO Data
| Chain | GOid | namespace | contents |
| A | 0000166 | molecular_function | nucleotide binding |
| A | 0000287 | molecular_function | magnesium ion binding |
| A | 0003824 | molecular_function | catalytic activity |
| A | 0004644 | molecular_function | phosphoribosylglycinamide formyltransferase activity |
| A | 0005515 | molecular_function | protein binding |
| A | 0005524 | molecular_function | ATP binding |
| A | 0005829 | cellular_component | cytosol |
| A | 0006164 | biological_process | purine nucleotide biosynthetic process |
| A | 0006189 | biological_process | 'de novo' IMP biosynthetic process |
| A | 0008776 | molecular_function | acetate kinase activity |
| A | 0009152 | biological_process | purine ribonucleotide biosynthetic process |
| A | 0016742 | molecular_function | hydroxymethyl-, formyl- and related transferase activity |
| A | 0016874 | molecular_function | ligase activity |
| A | 0043815 | molecular_function | phosphoribosylglycinamide formyltransferase 2 activity |
| A | 0046872 | molecular_function | metal ion binding |
| B | 0000166 | molecular_function | nucleotide binding |
| B | 0000287 | molecular_function | magnesium ion binding |
| B | 0003824 | molecular_function | catalytic activity |
| B | 0004644 | molecular_function | phosphoribosylglycinamide formyltransferase activity |
| B | 0005515 | molecular_function | protein binding |
| B | 0005524 | molecular_function | ATP binding |
| B | 0005829 | cellular_component | cytosol |
| B | 0006164 | biological_process | purine nucleotide biosynthetic process |
| B | 0006189 | biological_process | 'de novo' IMP biosynthetic process |
| B | 0008776 | molecular_function | acetate kinase activity |
| B | 0009152 | biological_process | purine ribonucleotide biosynthetic process |
| B | 0016742 | molecular_function | hydroxymethyl-, formyl- and related transferase activity |
| B | 0016874 | molecular_function | ligase activity |
| B | 0043815 | molecular_function | phosphoribosylglycinamide formyltransferase 2 activity |
| B | 0046872 | molecular_function | metal ion binding |
Functional Information from PDB Data
| site_id | AC1 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE MG A 393 |
| Chain | Residue |
| A | ADP1 |
| A | GLU267 |
| A | GLU279 |
| A | HOH485 |
| A | HOH841 |
| site_id | AC2 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE MG B 393 |
| Chain | Residue |
| B | HOH767 |
| B | GLU267 |
| B | GLU279 |
| B | ADP397 |
| B | HOH470 |
| site_id | AC3 |
| Number of Residues | 8 |
| Details | BINDING SITE FOR RESIDUE NA B 394 |
| Chain | Residue |
| A | ALA53 |
| A | HOH505 |
| A | HOH586 |
| A | HOH811 |
| A | HOH920 |
| B | MET50 |
| B | HIS51 |
| B | HOH555 |
| site_id | AC4 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE NA A 394 |
| Chain | Residue |
| A | ASN100 |
| A | VAL101 |
| A | PRO103 |
| A | HOH432 |
| A | HOH445 |
| A | HOH821 |
| site_id | AC5 |
| Number of Residues | 7 |
| Details | BINDING SITE FOR RESIDUE CL A 395 |
| Chain | Residue |
| A | ARG43 |
| A | VAL58 |
| A | ARG119 |
| A | ARG133 |
| A | PHE134 |
| A | HOH699 |
| A | HOH809 |
| site_id | AC6 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE CL A 396 |
| Chain | Residue |
| A | ARG43 |
| A | THR131 |
| A | TYR132 |
| A | HOH468 |
| site_id | AC7 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE CL B 395 |
| Chain | Residue |
| B | HIS216 |
| B | PHE217 |
| B | HOH488 |
| B | HOH644 |
| site_id | AC8 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE CL B 396 |
| Chain | Residue |
| A | HOH415 |
| B | PHE337 |
| B | GLY354 |
| site_id | AC9 |
| Number of Residues | 24 |
| Details | BINDING SITE FOR RESIDUE ADP A 1 |
| Chain | Residue |
| A | ARG114 |
| A | SER130 |
| A | ILE153 |
| A | LYS155 |
| A | GLN165 |
| A | GLU195 |
| A | GLY196 |
| A | VAL197 |
| A | VAL198 |
| A | PHE200 |
| A | GLU203 |
| A | GLN225 |
| A | GLU267 |
| A | PHE269 |
| A | GLU279 |
| A | MG393 |
| A | HOH465 |
| A | HOH479 |
| A | HOH485 |
| A | HOH552 |
| A | HOH556 |
| A | HOH595 |
| A | HOH760 |
| A | HOH841 |
| site_id | BC1 |
| Number of Residues | 24 |
| Details | BINDING SITE FOR RESIDUE ADP B 397 |
| Chain | Residue |
| B | ARG114 |
| B | SER130 |
| B | ILE153 |
| B | LYS155 |
| B | GLN165 |
| B | GLU195 |
| B | GLY196 |
| B | VAL198 |
| B | GLU203 |
| B | GLN225 |
| B | GLU267 |
| B | PHE269 |
| B | GLU279 |
| B | MG393 |
| B | HOH470 |
| B | HOH492 |
| B | HOH505 |
| B | HOH582 |
| B | HOH604 |
| B | HOH756 |
| B | HOH761 |
| B | HOH767 |
| B | HOH775 |
| B | HOH776 |
| site_id | BC2 |
| Number of Residues | 12 |
| Details | BINDING SITE FOR RESIDUE MPO A 397 |
| Chain | Residue |
| A | HOH688 |
| B | LEU8 |
| B | HIS54 |
| A | ASP46 |
| A | MET50 |
| A | HIS51 |
| A | ARG55 |
| A | SER56 |
| A | GLU143 |
| A | HOH460 |
| A | HOH500 |
| A | HOH509 |
| site_id | BC3 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE EDO A 398 |
| Chain | Residue |
| A | LEU34 |
| A | ARG305 |
| A | HOH438 |
| A | HOH629 |
| B | GLN349 |
| B | ILE350 |
| site_id | BC4 |
| Number of Residues | 11 |
| Details | BINDING SITE FOR RESIDUE EDO B 398 |
| Chain | Residue |
| A | EDO406 |
| A | HOH506 |
| A | HOH514 |
| B | GLU30 |
| B | ARG33 |
| B | ASP296 |
| B | LEU297 |
| B | SER298 |
| B | ALA301 |
| B | HOH406 |
| B | HOH482 |
| site_id | BC5 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE EDO A 399 |
| Chain | Residue |
| A | ILE378 |
| A | HOH934 |
| B | HOH627 |
| site_id | BC6 |
| Number of Residues | 9 |
| Details | BINDING SITE FOR RESIDUE EDO B 399 |
| Chain | Residue |
| B | GLY21 |
| B | GLU22 |
| B | LEU23 |
| B | GLY24 |
| B | GLU82 |
| B | HOH576 |
| B | HOH709 |
| B | HOH714 |
| B | HOH807 |
| site_id | BC7 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE EDO A 400 |
| Chain | Residue |
| A | ARG246 |
| A | GLU274 |
| A | VAL275 |
| A | HOH585 |
| A | HOH680 |
| site_id | BC8 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE EDO A 401 |
| Chain | Residue |
| A | ARG69 |
| A | HOH542 |
| A | HOH578 |
| A | HOH877 |
| site_id | BC9 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE EDO A 402 |
| Chain | Residue |
| A | THR2 |
| A | LEU3 |
| A | TYR78 |
| A | HOH549 |
| A | HOH700 |
| A | HOH765 |
| site_id | CC1 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE EDO B 400 |
| Chain | Residue |
| B | PRO328 |
| B | GLN329 |
| B | LEU330 |
| B | VAL390 |
| B | HOH409 |
| B | HOH483 |
| site_id | CC2 |
| Number of Residues | 8 |
| Details | BINDING SITE FOR RESIDUE EDO A 403 |
| Chain | Residue |
| A | ASN60 |
| A | ASP63 |
| A | ALA122 |
| A | THR129 |
| A | TYR132 |
| A | HOH568 |
| A | HOH571 |
| A | HOH898 |
| site_id | CC3 |
| Number of Residues | 7 |
| Details | BINDING SITE FOR RESIDUE EDO A 404 |
| Chain | Residue |
| A | GLU379 |
| A | HIS383 |
| A | HOH456 |
| A | HOH675 |
| A | HOH803 |
| A | HOH947 |
| A | HOH948 |
| site_id | CC4 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE EDO A 405 |
| Chain | Residue |
| A | ARG231 |
| A | HOH497 |
| A | HOH589 |
| A | HOH915 |
| A | HOH927 |
| site_id | CC5 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE EDO B 401 |
| Chain | Residue |
| B | PHE134 |
| B | ALA135 |
| B | LEU140 |
| B | ALA144 |
| B | HOH655 |
| B | HOH787 |
| site_id | CC6 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE EDO B 402 |
| Chain | Residue |
| B | LEU244 |
| B | GLU245 |
| B | GLN248 |
| B | HOH559 |
| B | HOH583 |
| site_id | CC7 |
| Number of Residues | 10 |
| Details | BINDING SITE FOR RESIDUE EDO A 406 |
| Chain | Residue |
| A | LEU292 |
| A | ILE293 |
| A | GLN349 |
| A | ARG351 |
| A | HOH452 |
| A | HOH478 |
| A | HOH514 |
| A | HOH843 |
| B | ASP296 |
| B | EDO398 |
| site_id | CC8 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE EDO A 407 |
| Chain | Residue |
| A | GLY64 |
| A | ALA87 |
| A | MET90 |
| A | GLN93 |
Functional Information from SwissProt/UniProt
| site_id | SWS_FT_FI1 |
| Number of Residues | 24 |
| Details | BINDING: BINDING => ECO:0000255|HAMAP-Rule:MF_01643, ECO:0000269|PubMed:10913290, ECO:0000269|PubMed:11953435 |
| Chain | Residue | Details |
| A | LEU23 | |
| A | THR287 | |
| A | PRO356 | |
| A | ARG363 | |
| B | LEU23 | |
| B | ILE83 | |
| B | GLU115 | |
| B | PRO156 | |
| B | SER161 | |
| B | GLY196 | |
| B | ILE204 | |
| A | ILE83 | |
| B | LEU268 | |
| B | VAL280 | |
| B | THR287 | |
| B | PRO356 | |
| B | ARG363 | |
| A | GLU115 | |
| A | PRO156 | |
| A | SER161 | |
| A | GLY196 | |
| A | ILE204 | |
| A | LEU268 | |
| A | VAL280 |
| site_id | SWS_FT_FI2 |
| Number of Residues | 2 |
| Details | MOD_RES: N6-acetyllysine => ECO:0000269|PubMed:18723842 |
| Chain | Residue | Details |
| A | TYR180 | |
| B | TYR180 |
Catalytic Information from CSA
| site_id | MCSA1 |
| Number of Residues | 7 |
| Details | M-CSA 665 |
| Chain | Residue | Details |
| A | SER161 | electrostatic stabiliser, hydrogen bond donor |
| A | LYS163 | electrostatic stabiliser, hydrogen bond donor |
| A | LEU268 | electrostatic stabiliser, metal ligand |
| A | VAL280 | electrostatic stabiliser, metal ligand |
| A | THR287 | hydrogen bond acceptor, hydrogen bond donor, metal ligand, proton acceptor, proton donor |
| A | GLY288 | electrostatic stabiliser, hydrogen bond donor |
| A | LEU364 | electrostatic stabiliser, hydrogen bond donor |
| site_id | MCSA2 |
| Number of Residues | 7 |
| Details | M-CSA 665 |
| Chain | Residue | Details |
| B | SER161 | electrostatic stabiliser, hydrogen bond donor |
| B | LYS163 | electrostatic stabiliser, hydrogen bond donor |
| B | LEU268 | electrostatic stabiliser, metal ligand |
| B | VAL280 | electrostatic stabiliser, metal ligand |
| B | THR287 | hydrogen bond acceptor, hydrogen bond donor, metal ligand, proton acceptor, proton donor |
| B | GLY288 | electrostatic stabiliser, hydrogen bond donor |
| B | LEU364 | electrostatic stabiliser, hydrogen bond donor |
