5FY8
Crystal structure of human JMJD2A in complex with D-threo-isocitrate
Functional Information from PDB Data
| site_id | AC1 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE NI A 501 |
| Chain | Residue |
| A | HIS188 |
| A | GLU190 |
| A | HIS276 |
| A | N811354 |
| A | HOH2050 |
| site_id | AC2 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE ZN A 502 |
| Chain | Residue |
| A | CYS234 |
| A | HIS240 |
| A | CYS306 |
| A | CYS308 |
| site_id | AC3 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE NI B 501 |
| Chain | Residue |
| B | HIS188 |
| B | GLU190 |
| B | HIS276 |
| B | N811354 |
| B | HOH2048 |
| site_id | AC4 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE ZN B 502 |
| Chain | Residue |
| B | CYS234 |
| B | HIS240 |
| B | CYS306 |
| B | CYS308 |
| site_id | AC5 |
| Number of Residues | 13 |
| Details | BINDING SITE FOR RESIDUE N81 A 1354 |
| Chain | Residue |
| A | TYR132 |
| A | TYR177 |
| A | PHE185 |
| A | HIS188 |
| A | GLU190 |
| A | SER196 |
| A | ASN198 |
| A | TRP208 |
| A | LYS241 |
| A | HIS276 |
| A | SER288 |
| A | NI501 |
| A | HOH2050 |
| site_id | AC6 |
| Number of Residues | 13 |
| Details | BINDING SITE FOR RESIDUE N81 B 1354 |
| Chain | Residue |
| B | TYR132 |
| B | TYR177 |
| B | PHE185 |
| B | HIS188 |
| B | GLU190 |
| B | SER196 |
| B | ASN198 |
| B | LYS206 |
| B | TRP208 |
| B | HIS276 |
| B | SER288 |
| B | NI501 |
| B | HOH2048 |
| site_id | AC7 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE DMS A 1355 |
| Chain | Residue |
| A | PHE227 |
| A | PRO228 |
| A | GLY229 |
| A | SER230 |
| A | HOH2068 |
| B | LYS105 |
| site_id | AC8 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE DMS B 1355 |
| Chain | Residue |
| A | LYS105 |
| B | PHE226 |
| B | PHE227 |
| B | PRO228 |
| B | GLY229 |
| B | SER230 |
| site_id | AC9 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE EDO B 1356 |
| Chain | Residue |
| B | GLU235 |
| B | ALA236 |
| B | PHE237 |
| B | LEU238 |
| B | HOH2059 |
| B | HOH2071 |
| site_id | BC1 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE EDO A 1356 |
| Chain | Residue |
| A | CYS234 |
| A | GLU235 |
| A | ALA236 |
| A | PHE237 |
| A | LEU238 |
| A | HOH2085 |
| site_id | BC2 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE EDO A 1357 |
| Chain | Residue |
| A | LEU65 |
| A | GLY138 |
| A | THR139 |
| site_id | BC3 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE EDO B 1357 |
| Chain | Residue |
| B | ARG295 |
| B | ASP342 |
| B | LEU345 |
| B | HOH2073 |
| site_id | BC4 |
| Number of Residues | 8 |
| Details | BINDING SITE FOR RESIDUE EDO B 1358 |
| Chain | Residue |
| B | ASP191 |
| B | MET192 |
| B | ARG239 |
| B | LEU305 |
| B | CYS306 |
| B | MET312 |
| B | VAL313 |
| B | HOH2076 |
| site_id | BC5 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE EDO A 1358 |
| Chain | Residue |
| A | TYR253 |
| A | GLY254 |
| A | HOH2077 |
| A | HOH2108 |
| B | LYS259 |
| B | VAL260 |
| site_id | BC6 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE EDO B 1359 |
| Chain | Residue |
| B | ILE67 |
| B | PRO68 |
| B | ALA69 |
| B | ALA134 |
| B | ASP135 |
| B | VAL136 |
Functional Information from SwissProt/UniProt
| site_id | SWS_FT_FI1 |
| Number of Residues | 84 |
| Details | Domain: {"description":"JmjN","evidences":[{"source":"PROSITE-ProRule","id":"PRU00537","evidenceCode":"ECO:0000255"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI2 |
| Number of Residues | 332 |
| Details | Domain: {"description":"JmjC","evidences":[{"source":"PROSITE-ProRule","id":"PRU00538","evidenceCode":"ECO:0000255"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI3 |
| Number of Residues | 6 |
| Details | Binding site: {"evidences":[{"source":"PubMed","id":"16677698","evidenceCode":"ECO:0000269"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI4 |
| Number of Residues | 4 |
| Details | Binding site: {"evidences":[{"source":"PROSITE-ProRule","id":"PRU00538","evidenceCode":"ECO:0000255"},{"source":"PubMed","id":"16677698","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"26741168","evidenceCode":"ECO:0000305"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI5 |
| Number of Residues | 2 |
| Details | Binding site: {"evidences":[{"source":"PubMed","id":"16677698","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"26741168","evidenceCode":"ECO:0000305"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI6 |
| Number of Residues | 8 |
| Details | Binding site: {"evidences":[{"source":"PDB","id":"5F2W","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"5F32","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"5F37","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"5F39","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"5F3E","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"5F3G","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"5F5I","evidenceCode":"ECO:0007744"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI7 |
| Number of Residues | 2 |
| Details | Binding site: {"evidences":[{"source":"UniProtKB","id":"B2RXH2","evidenceCode":"ECO:0000250"}]} |
| Chain | Residue | Details |
Catalytic Information from CSA
| site_id | MCSA1 |
| Number of Residues | 6 |
| Details | M-CSA 370 |
| Chain | Residue | Details |
| A | GLY170 | hydrogen bond acceptor, steric role |
| A | TYR177 | hydrogen bond donor, steric role |
| A | HIS188 | metal ligand |
| A | GLU190 | attractive charge-charge interaction, hydrogen bond acceptor, metal ligand, steric role |
| A | HIS276 | metal ligand |
| A | SER288 | hydrogen bond donor, steric role |
| site_id | MCSA2 |
| Number of Residues | 6 |
| Details | M-CSA 370 |
| Chain | Residue | Details |
| B | GLY170 | hydrogen bond acceptor, steric role |
| B | TYR177 | hydrogen bond donor, steric role |
| B | HIS188 | metal ligand |
| B | GLU190 | attractive charge-charge interaction, hydrogen bond acceptor, metal ligand, steric role |
| B | HIS276 | metal ligand |
| B | SER288 | hydrogen bond donor, steric role |
