6G5W
Crystal Structure of KDM4A with compound YP-03-038
Functional Information from PDB Data
| site_id | AC1 |
| Number of Residues | 4 |
| Details | binding site for residue ZN A 401 |
| Chain | Residue |
| A | CYS234 |
| A | HIS240 |
| A | CYS306 |
| A | CYS308 |
| site_id | AC2 |
| Number of Residues | 3 |
| Details | binding site for residue NI A 402 |
| Chain | Residue |
| A | HIS215 |
| A | HOH707 |
| A | HOH712 |
| site_id | AC3 |
| Number of Residues | 6 |
| Details | binding site for residue NI A 403 |
| Chain | Residue |
| A | HIS276 |
| A | CIT406 |
| A | HOH502 |
| A | HOH571 |
| A | HIS188 |
| A | GLU190 |
| site_id | AC4 |
| Number of Residues | 6 |
| Details | binding site for residue EDO A 404 |
| Chain | Residue |
| A | GLU235 |
| A | ALA236 |
| A | PHE237 |
| A | LEU238 |
| A | HOH511 |
| A | HOH525 |
| site_id | AC5 |
| Number of Residues | 5 |
| Details | binding site for residue EDO A 405 |
| Chain | Residue |
| A | THR139 |
| A | TYR141 |
| A | HOH518 |
| A | HOH607 |
| A | HOH714 |
| site_id | AC6 |
| Number of Residues | 16 |
| Details | binding site for residue CIT A 406 |
| Chain | Residue |
| A | TYR132 |
| A | TYR177 |
| A | PHE185 |
| A | HIS188 |
| A | ASN198 |
| A | LYS206 |
| A | TRP208 |
| A | HIS276 |
| A | ALA286 |
| A | NI403 |
| A | HOH502 |
| A | HOH560 |
| A | HOH571 |
| A | HOH573 |
| A | HOH603 |
| A | HOH667 |
| site_id | AC7 |
| Number of Residues | 10 |
| Details | binding site for residue CIT A 407 |
| Chain | Residue |
| A | GLU214 |
| A | HIS215 |
| A | ARG218 |
| A | HOH506 |
| A | HOH568 |
| B | GLU115 |
| B | LYS259 |
| B | NI403 |
| B | ENZ407 |
| B | HOH661 |
| site_id | AC8 |
| Number of Residues | 4 |
| Details | binding site for residue ZN B 401 |
| Chain | Residue |
| B | CYS234 |
| B | HIS240 |
| B | CYS306 |
| B | CYS308 |
| site_id | AC9 |
| Number of Residues | 6 |
| Details | binding site for residue NI B 402 |
| Chain | Residue |
| B | HIS188 |
| B | GLU190 |
| B | HIS276 |
| B | CIT406 |
| B | HOH501 |
| B | HOH544 |
| site_id | AD1 |
| Number of Residues | 3 |
| Details | binding site for residue NI B 403 |
| Chain | Residue |
| A | CIT407 |
| B | ENZ407 |
| B | HOH661 |
| site_id | AD2 |
| Number of Residues | 3 |
| Details | binding site for residue NA B 404 |
| Chain | Residue |
| B | ASN26 |
| B | SER28 |
| B | HOH651 |
| site_id | AD3 |
| Number of Residues | 4 |
| Details | binding site for residue EDO B 405 |
| Chain | Residue |
| A | ARG95 |
| B | TYR59 |
| B | ARG98 |
| B | PHE283 |
| site_id | AD4 |
| Number of Residues | 16 |
| Details | binding site for residue CIT B 406 |
| Chain | Residue |
| B | TYR132 |
| B | TYR177 |
| B | PHE185 |
| B | HIS188 |
| B | ASN198 |
| B | LYS206 |
| B | TRP208 |
| B | HIS276 |
| B | ALA286 |
| B | NI402 |
| B | HOH501 |
| B | HOH537 |
| B | HOH544 |
| B | HOH623 |
| B | HOH631 |
| B | HOH647 |
| site_id | AD5 |
| Number of Residues | 14 |
| Details | binding site for residue ENZ B 407 |
| Chain | Residue |
| B | HOH661 |
| A | HIS215 |
| A | CIT407 |
| B | PHE114 |
| B | GLU115 |
| B | GLU118 |
| B | SER207 |
| B | TRP208 |
| B | TYR209 |
| B | LYS259 |
| B | VAL260 |
| B | THR261 |
| B | NI403 |
| B | HOH634 |
Functional Information from SwissProt/UniProt
| site_id | SWS_FT_FI1 |
| Number of Residues | 6 |
| Details | BINDING: BINDING => ECO:0000269|PubMed:16677698 |
| Chain | Residue | Details |
| A | TYR132 | |
| A | ASN198 | |
| A | LYS206 | |
| B | TYR132 | |
| B | ASN198 | |
| B | LYS206 |
| site_id | SWS_FT_FI2 |
| Number of Residues | 4 |
| Details | BINDING: BINDING => ECO:0000255|PROSITE-ProRule:PRU00538, ECO:0000269|PubMed:16677698, ECO:0000305|PubMed:26741168 |
| Chain | Residue | Details |
| A | HIS188 | |
| A | HIS276 | |
| B | HIS188 | |
| B | HIS276 |
| site_id | SWS_FT_FI3 |
| Number of Residues | 2 |
| Details | BINDING: BINDING => ECO:0000269|PubMed:16677698, ECO:0000305|PubMed:26741168 |
| Chain | Residue | Details |
| A | GLU190 | |
| B | GLU190 |
| site_id | SWS_FT_FI4 |
| Number of Residues | 8 |
| Details | BINDING: BINDING => ECO:0007744|PDB:5F2W, ECO:0007744|PDB:5F32, ECO:0007744|PDB:5F37, ECO:0007744|PDB:5F39, ECO:0007744|PDB:5F3E, ECO:0007744|PDB:5F3G, ECO:0007744|PDB:5F5I |
| Chain | Residue | Details |
| A | CYS234 | |
| A | HIS240 | |
| A | CYS306 | |
| A | CYS308 | |
| B | CYS234 | |
| B | HIS240 | |
| B | CYS306 | |
| B | CYS308 |
| site_id | SWS_FT_FI5 |
| Number of Residues | 2 |
| Details | BINDING: BINDING => ECO:0000250|UniProtKB:B2RXH2 |
| Chain | Residue | Details |
| A | LYS241 | |
| B | LYS241 |
| site_id | SWS_FT_FI6 |
| Number of Residues | 2 |
| Details | MOD_RES: N-acetylalanine => ECO:0007744|PubMed:19413330 |
| Chain | Residue | Details |
| A | ALA2 | |
| B | ALA2 |
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 |
