1KJI
Crystal structure of glycinamide ribonucleotide transformylase in complex with Mg-AMPPCP
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 | 4 |
| Details | BINDING SITE FOR RESIDUE MG A 393 |
| Chain | Residue |
| A | ACP1 |
| A | GLU279 |
| A | HOH509 |
| A | HOH536 |
| site_id | AC2 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE MG A 394 |
| Chain | Residue |
| A | ACP1 |
| A | GLU267 |
| A | GLU279 |
| A | HOH465 |
| site_id | AC3 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE MG B 393 |
| Chain | Residue |
| B | ACP396 |
| B | HOH470 |
| B | HOH547 |
| B | GLU279 |
| site_id | AC4 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE MG B 394 |
| Chain | Residue |
| B | GLU267 |
| B | GLU279 |
| B | ACP396 |
| B | HOH635 |
| site_id | AC5 |
| Number of Residues | 7 |
| Details | BINDING SITE FOR RESIDUE NA A 395 |
| Chain | Residue |
| A | ALA53 |
| A | HOH453 |
| A | HOH521 |
| B | ALA53 |
| B | HOH456 |
| B | HOH651 |
| B | HOH745 |
| site_id | AC6 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE NA A 396 |
| Chain | Residue |
| A | GLU95 |
| A | ASN100 |
| A | VAL101 |
| A | HOH567 |
| A | HOH637 |
| site_id | AC7 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE NA B 395 |
| Chain | Residue |
| B | ASN100 |
| B | VAL101 |
| B | PRO103 |
| B | HOH461 |
| B | HOH690 |
| site_id | AC8 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE CL A 397 |
| Chain | Residue |
| A | ARG43 |
| A | VAL58 |
| A | ARG119 |
| A | ARG133 |
| A | PHE134 |
| A | HOH590 |
| site_id | AC9 |
| Number of Residues | 26 |
| Details | BINDING SITE FOR RESIDUE ACP A 1 |
| Chain | Residue |
| A | ARG114 |
| A | ILE153 |
| A | LYS155 |
| A | SER160 |
| A | SER161 |
| A | GLY162 |
| A | GLN165 |
| A | GLU195 |
| A | GLY196 |
| A | VAL198 |
| A | GLU203 |
| A | GLN225 |
| A | GLU267 |
| A | PHE269 |
| A | GLU279 |
| A | MG393 |
| A | MG394 |
| A | HOH432 |
| A | HOH465 |
| A | HOH475 |
| A | HOH485 |
| A | HOH509 |
| A | HOH562 |
| A | HOH563 |
| A | HOH644 |
| A | HOH758 |
| site_id | BC1 |
| Number of Residues | 20 |
| Details | BINDING SITE FOR RESIDUE ACP B 396 |
| Chain | Residue |
| B | ARG114 |
| B | SER130 |
| B | LYS155 |
| B | SER159 |
| B | SER160 |
| B | SER161 |
| B | GLY162 |
| B | GLU195 |
| B | GLY196 |
| B | VAL198 |
| B | GLU203 |
| B | GLU267 |
| B | GLU279 |
| B | MG393 |
| B | MG394 |
| B | HOH547 |
| B | HOH553 |
| B | HOH572 |
| B | HOH635 |
| B | HOH767 |
| site_id | BC2 |
| Number of Residues | 13 |
| Details | BINDING SITE FOR RESIDUE MPO A 398 |
| Chain | Residue |
| A | ASP46 |
| A | MET50 |
| A | HIS51 |
| A | ARG55 |
| A | SER56 |
| A | GLU143 |
| A | HOH437 |
| A | HOH453 |
| A | HOH468 |
| A | HOH685 |
| A | HOH727 |
| B | LEU8 |
| B | HIS54 |
| site_id | BC3 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE EDO A 399 |
| Chain | Residue |
| A | THR129 |
| A | SER130 |
| A | THR131 |
| A | TYR132 |
| A | HOH502 |
| A | ASP63 |
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 |
