6HGT
Crystal structure of human KDM4A complexed with co-substrate analog NOG and histone H3 peptide with K9R mutation
Functional Information from PDB Data
| site_id | AC1 |
| Number of Residues | 4 |
| Details | binding site for residue ZN A 401 |
| Chain | Residue |
| A | HIS188 |
| A | GLU190 |
| A | HIS276 |
| A | OGA403 |
| site_id | AC2 |
| Number of Residues | 4 |
| Details | binding site for residue ZN A 402 |
| Chain | Residue |
| A | CYS234 |
| A | HIS240 |
| A | CYS306 |
| A | CYS308 |
| site_id | AC3 |
| Number of Residues | 11 |
| Details | binding site for residue OGA A 403 |
| Chain | Residue |
| A | PHE185 |
| A | HIS188 |
| A | GLU190 |
| A | SER196 |
| A | ASN198 |
| A | LYS206 |
| A | HIS276 |
| A | SER288 |
| A | ZN401 |
| A | HOH505 |
| A | TYR132 |
| site_id | AC4 |
| Number of Residues | 5 |
| Details | binding site for residue ZN B 401 |
| Chain | Residue |
| B | HIS188 |
| B | GLU190 |
| B | HIS276 |
| B | OGA403 |
| B | HOH582 |
| site_id | AC5 |
| Number of Residues | 4 |
| Details | binding site for residue ZN B 402 |
| Chain | Residue |
| B | CYS234 |
| B | HIS240 |
| B | CYS306 |
| B | CYS308 |
| site_id | AC6 |
| Number of Residues | 11 |
| Details | binding site for residue OGA B 403 |
| Chain | Residue |
| B | TYR132 |
| B | PHE185 |
| B | HIS188 |
| B | GLU190 |
| B | SER196 |
| B | ASN198 |
| B | LYS206 |
| B | HIS276 |
| B | SER288 |
| B | ZN401 |
| B | HOH521 |
| site_id | AC7 |
| Number of Residues | 5 |
| Details | binding site for residue ZN C 401 |
| Chain | Residue |
| C | HIS188 |
| C | GLU190 |
| C | HIS276 |
| C | OGA403 |
| C | HOH530 |
| site_id | AC8 |
| Number of Residues | 4 |
| Details | binding site for residue ZN C 402 |
| Chain | Residue |
| C | CYS234 |
| C | HIS240 |
| C | CYS306 |
| C | CYS308 |
| site_id | AC9 |
| Number of Residues | 12 |
| Details | binding site for residue OGA C 403 |
| Chain | Residue |
| C | TYR132 |
| C | PHE185 |
| C | HIS188 |
| C | GLU190 |
| C | SER196 |
| C | ASN198 |
| C | LYS206 |
| C | HIS276 |
| C | SER288 |
| C | ZN401 |
| G | ARG9 |
| G | HOH102 |
| site_id | AD1 |
| Number of Residues | 4 |
| Details | binding site for residue ZN D 401 |
| Chain | Residue |
| D | HIS188 |
| D | GLU190 |
| D | HIS276 |
| D | OGA403 |
| site_id | AD2 |
| Number of Residues | 4 |
| Details | binding site for residue ZN D 402 |
| Chain | Residue |
| D | CYS234 |
| D | HIS240 |
| D | CYS306 |
| D | CYS308 |
| site_id | AD3 |
| Number of Residues | 12 |
| Details | binding site for residue OGA D 403 |
| Chain | Residue |
| D | TYR132 |
| D | PHE185 |
| D | HIS188 |
| D | GLU190 |
| D | SER196 |
| D | ASN198 |
| D | LYS206 |
| D | HIS276 |
| D | SER288 |
| D | ZN401 |
| D | HOH504 |
| H | ARG9 |
Functional Information from SwissProt/UniProt
| site_id | SWS_FT_FI1 |
| Number of Residues | 4 |
| Details | MOD_RES: Phosphothreonine; by HASPIN and VRK1 => ECO:0000269|PubMed:15681610, ECO:0000269|PubMed:16185088, ECO:0000269|PubMed:31527692 |
| Chain | Residue | Details |
| C | LYS206 | |
| D | TYR132 | |
| D | ASN198 | |
| D | LYS206 | |
| B | ASN198 | |
| B | LYS206 | |
| C | TYR132 | |
| C | ASN198 | |
| E | THR3 | |
| F | THR3 | |
| G | THR3 | |
| H | THR3 |
| site_id | SWS_FT_FI2 |
| Number of Residues | 4 |
| Details | MOD_RES: N6-methyllysine; alternate => ECO:0000269|PubMed:16267050, ECO:0000269|PubMed:16457588, ECO:0000269|PubMed:17194708 |
| Chain | Residue | Details |
| F | LYS4 | |
| G | LYS4 | |
| H | LYS4 | |
| C | HIS188 | |
| C | HIS276 | |
| D | HIS188 | |
| D | HIS276 | |
| E | LYS4 |
| site_id | SWS_FT_FI3 |
| Number of Residues | 4 |
| Details | MOD_RES: 5-glutamyl serotonin; alternate => ECO:0000269|PubMed:30867594 |
| Chain | Residue | Details |
| E | GLN5 | |
| F | GLN5 | |
| G | GLN5 | |
| H | GLN5 |
| site_id | SWS_FT_FI4 |
| Number of Residues | 4 |
| Details | MOD_RES: Phosphothreonine; by PKC => ECO:0000269|PubMed:20228790 |
| Chain | Residue | Details |
| B | CYS234 | |
| B | HIS240 | |
| B | CYS306 | |
| B | CYS308 | |
| C | CYS234 | |
| C | HIS240 | |
| C | CYS306 | |
| C | CYS308 | |
| D | CYS234 | |
| D | HIS240 | |
| D | CYS306 | |
| D | CYS308 | |
| E | THR6 | |
| F | THR6 | |
| G | THR6 | |
| H | THR6 |
| site_id | SWS_FT_FI5 |
| Number of Residues | 4 |
| Details | MOD_RES: Symmetric dimethylarginine; by PRMT5; alternate => ECO:0000250|UniProtKB:P68433 |
| Chain | Residue | Details |
| E | ARG8 | |
| F | ARG8 | |
| G | ARG8 | |
| H | ARG8 |
| site_id | SWS_FT_FI6 |
| Number of Residues | 4 |
| Details | MOD_RES: N6-methyllysine; alternate => ECO:0000269|PubMed:11242053, ECO:0000269|PubMed:16185088, ECO:0000269|PubMed:16267050, ECO:0000269|PubMed:16457588, ECO:0000269|PubMed:17194708 |
| Chain | Residue | Details |
| E | ARG9 | |
| F | ARG9 | |
| G | ARG9 | |
| H | ARG9 |
| site_id | SWS_FT_FI7 |
| Number of Residues | 4 |
| Details | MOD_RES: Phosphoserine; alternate; by AURKB, AURKC, RPS6KA3, RPS6KA4 and RPS6KA5 => ECO:0000269|PubMed:10464286, ECO:0000269|PubMed:11856369, ECO:0000269|PubMed:12560483, ECO:0000269|PubMed:15681610, ECO:0000269|PubMed:16185088, ECO:0000269|PubMed:16457588 |
| Chain | Residue | Details |
| E | SER10 | |
| F | SER10 | |
| G | SER10 | |
| H | SER10 |
| site_id | SWS_FT_FI8 |
| Number of Residues | 4 |
| Details | MOD_RES: Phosphothreonine; by PKC and CHEK1 => ECO:0000269|PubMed:12560483, ECO:0000269|PubMed:18066052, ECO:0000269|PubMed:18243098, ECO:0000269|PubMed:22901803 |
| Chain | Residue | Details |
| H | THR11 | |
| E | THR11 | |
| F | THR11 | |
| G | THR11 |
| site_id | SWS_FT_FI9 |
| Number of Residues | 4 |
| Details | MOD_RES: N6-succinyllysine; alternate => ECO:0000269|PubMed:22389435 |
| Chain | Residue | Details |
| G | LYS14 | |
| H | LYS14 | |
| E | LYS14 | |
| F | LYS14 |
| site_id | SWS_FT_FI10 |
| Number of Residues | 4 |
| Details | MOD_RES: Citrulline; alternate => ECO:0000269|PubMed:15345777, ECO:0000269|PubMed:16497732, ECO:0000269|PubMed:16567635 |
| Chain | Residue | Details |
| E | ARG17 | |
| F | ARG17 | |
| G | ARG17 | |
| H | ARG17 |
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 |
| site_id | MCSA3 |
| Number of Residues | 6 |
| Details | M-CSA 370 |
| Chain | Residue | Details |
| C | GLY170 | hydrogen bond acceptor, steric role |
| C | TYR177 | hydrogen bond donor, steric role |
| C | HIS188 | metal ligand |
| C | GLU190 | attractive charge-charge interaction, hydrogen bond acceptor, metal ligand, steric role |
| C | HIS276 | metal ligand |
| C | SER288 | hydrogen bond donor, steric role |
| site_id | MCSA4 |
| Number of Residues | 6 |
| Details | M-CSA 370 |
| Chain | Residue | Details |
| D | GLY170 | hydrogen bond acceptor, steric role |
| D | TYR177 | hydrogen bond donor, steric role |
| D | HIS188 | metal ligand |
| D | GLU190 | attractive charge-charge interaction, hydrogen bond acceptor, metal ligand, steric role |
| D | HIS276 | metal ligand |
| D | SER288 | hydrogen bond donor, steric role |
