4HON
Crystal structure of human JMJD2D/KDM4D in complex with an H3K9me3 peptide and 2-oxoglutarate
Functional Information from PDB Data
| site_id | AC1 |
| Number of Residues | 14 |
| Details | BINDING SITE FOR RESIDUE AKG A 401 |
| Chain | Residue |
| A | TYR136 |
| A | NI402 |
| A | PDO415 |
| A | HOH507 |
| F | M3L9 |
| F | HOH101 |
| A | PHE189 |
| A | HIS192 |
| A | GLU194 |
| A | SER200 |
| A | ASN202 |
| A | LYS210 |
| A | TRP212 |
| A | HIS280 |
| site_id | AC2 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE NI A 402 |
| Chain | Residue |
| A | HIS192 |
| A | GLU194 |
| A | HIS280 |
| A | AKG401 |
| A | HOH507 |
| site_id | AC3 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE ZN A 403 |
| Chain | Residue |
| A | CYS238 |
| A | HIS244 |
| A | CYS310 |
| A | CYS312 |
| site_id | AC4 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE SCN A 404 |
| Chain | Residue |
| A | LYS150 |
| A | GLN151 |
| A | SCN406 |
| site_id | AC5 |
| Number of Residues | 1 |
| Details | BINDING SITE FOR RESIDUE SCN A 405 |
| Chain | Residue |
| A | GLU27 |
| site_id | AC6 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE SCN A 406 |
| Chain | Residue |
| A | LYS58 |
| A | THR149 |
| A | SCN404 |
| site_id | AC7 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE NO3 A 407 |
| Chain | Residue |
| A | GLU224 |
| A | ALA240 |
| A | PHE241 |
| A | LEU242 |
| A | HOH664 |
| A | HOH683 |
| site_id | AC8 |
| Number of Residues | 7 |
| Details | BINDING SITE FOR RESIDUE NO3 A 408 |
| Chain | Residue |
| A | LYS305 |
| A | ARG332 |
| A | LEU335 |
| A | TRP336 |
| A | HOH549 |
| B | ASP302 |
| B | MET306 |
| site_id | AC9 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE NO3 A 409 |
| Chain | Residue |
| A | LYS305 |
| A | MET321 |
| A | TRP336 |
| A | GLN340 |
| A | HOH630 |
| A | HOH652 |
| site_id | BC1 |
| Number of Residues | 8 |
| Details | BINDING SITE FOR RESIDUE NO3 A 410 |
| Chain | Residue |
| A | ASP302 |
| A | MET306 |
| A | HOH602 |
| A | HOH697 |
| B | LYS305 |
| B | ARG332 |
| B | LEU335 |
| B | TRP336 |
| site_id | BC2 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE NO3 A 411 |
| Chain | Residue |
| A | GLU314 |
| A | ALA315 |
| A | ARG316 |
| A | VAL317 |
| F | ALA7 |
| F | ARG8 |
| site_id | BC3 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE NO3 A 412 |
| Chain | Residue |
| A | PRO113 |
| A | LYS124 |
| A | ASN128 |
| A | TRP185 |
| A | LYS186 |
| A | HOH510 |
| site_id | BC4 |
| Number of Residues | 1 |
| Details | BINDING SITE FOR RESIDUE NO3 A 413 |
| Chain | Residue |
| A | HOH720 |
| site_id | BC5 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE NO3 A 414 |
| Chain | Residue |
| A | SER67 |
| A | VAL98 |
| A | GLY99 |
| A | ARG102 |
| site_id | BC6 |
| Number of Residues | 10 |
| Details | BINDING SITE FOR RESIDUE PDO A 415 |
| Chain | Residue |
| A | PHE189 |
| A | ALA190 |
| A | HIS192 |
| A | LYS245 |
| A | AKG401 |
| A | HOH507 |
| A | HOH537 |
| F | SER10 |
| F | THR11 |
| F | HOH101 |
| site_id | BC7 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE PDO A 416 |
| Chain | Residue |
| A | THR87 |
| A | TYR89 |
| A | PHE231 |
| A | PRO232 |
| A | HOH536 |
| A | HOH561 |
| site_id | BC8 |
| Number of Residues | 2 |
| Details | BINDING SITE FOR RESIDUE PDO A 417 |
| Chain | Residue |
| A | GLY142 |
| A | SER143 |
| site_id | BC9 |
| Number of Residues | 7 |
| Details | BINDING SITE FOR RESIDUE PDO A 418 |
| Chain | Residue |
| A | MET19 |
| A | ILE20 |
| B | ILE20 |
| B | PHE21 |
| B | HIS22 |
| B | TYR34 |
| B | HOH570 |
| site_id | CC1 |
| Number of Residues | 14 |
| Details | BINDING SITE FOR RESIDUE AKG B 401 |
| Chain | Residue |
| B | TYR136 |
| B | PHE189 |
| B | HIS192 |
| B | GLU194 |
| B | SER200 |
| B | ASN202 |
| B | LYS210 |
| B | TRP212 |
| B | HIS280 |
| B | ALA292 |
| B | NI402 |
| B | HOH508 |
| B | HOH524 |
| G | M3L9 |
| site_id | CC2 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE NI B 402 |
| Chain | Residue |
| B | HIS192 |
| B | GLU194 |
| B | HIS280 |
| B | AKG401 |
| B | HOH508 |
| site_id | CC3 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE ZN B 403 |
| Chain | Residue |
| B | CYS238 |
| B | HIS244 |
| B | CYS310 |
| B | CYS312 |
| site_id | CC4 |
| Number of Residues | 2 |
| Details | BINDING SITE FOR RESIDUE SCN B 404 |
| Chain | Residue |
| B | ARG60 |
| B | ASN65 |
| site_id | CC5 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE SCN B 405 |
| Chain | Residue |
| B | LYS58 |
| B | THR149 |
| B | HOH655 |
| site_id | CC6 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE SCN B 406 |
| Chain | Residue |
| A | GLU68 |
| B | LYS124 |
| B | ASN128 |
| B | HOH576 |
| site_id | CC7 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE NO3 B 407 |
| Chain | Residue |
| B | GLU224 |
| B | ALA240 |
| B | PHE241 |
| B | LEU242 |
| site_id | CC8 |
| Number of Residues | 8 |
| Details | BINDING SITE FOR RESIDUE NO3 B 408 |
| Chain | Residue |
| A | PRO217 |
| A | GLU218 |
| A | TYR277 |
| A | TYR303 |
| A | HOH625 |
| B | ASP334 |
| B | LEU335 |
| B | ARG338 |
| site_id | CC9 |
| Number of Residues | 8 |
| Details | BINDING SITE FOR RESIDUE NO3 B 409 |
| Chain | Residue |
| A | ASP334 |
| A | LEU335 |
| A | ARG338 |
| B | PRO217 |
| B | GLU218 |
| B | TYR277 |
| B | TYR303 |
| B | HOH594 |
| site_id | DC1 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE NO3 B 410 |
| Chain | Residue |
| B | LYS124 |
| B | ASN128 |
| B | TRP185 |
| B | LYS186 |
| B | HOH521 |
| B | HOH584 |
| site_id | DC2 |
| Number of Residues | 2 |
| Details | BINDING SITE FOR RESIDUE PDO B 411 |
| Chain | Residue |
| B | ILE140 |
| B | SER143 |
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 | 8 |
| Details | Binding site: {"evidences":[{"source":"UniProtKB","id":"B2RXH2","evidenceCode":"ECO:0000250"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI4 |
| Number of Residues | 6 |
| Details | Binding site: {"evidences":[{"source":"PROSITE-ProRule","id":"PRU00538","evidenceCode":"ECO:0000255"},{"source":"PubMed","id":"26741168","evidenceCode":"ECO:0000305"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI5 |
| Number of Residues | 8 |
| Details | Binding site: {"evidences":[{"source":"PDB","id":"5F5A","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"5F5C","evidenceCode":"ECO:0007744"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI6 |
| Number of Residues | 4 |
| Details | Modified residue: {"description":"PolyADP-ribosyl glutamic acid","evidences":[{"source":"PubMed","id":"23102699","evidenceCode":"ECO:0000269"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI7 |
| Number of Residues | 1 |
| Details | Modified residue: {"description":"Phosphoserine; alternate; by AURKB, AURKC, RPS6KA3, RPS6KA4 and RPS6KA5","evidences":[{"source":"PubMed","id":"10464286","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"11856369","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"12560483","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"15681610","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"16185088","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"16457588","evidenceCode":"ECO:0000269"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI8 |
| Number of Residues | 1 |
| Details | Modified residue: {"description":"Phosphothreonine; by PKC and CHEK1","evidences":[{"source":"PubMed","id":"12560483","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"18066052","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"18243098","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"22901803","evidenceCode":"ECO:0000269"}]} |
| Chain | Residue | Details |
