Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 574 |
| PDBID: | 3LD8 |
| Chains: | CB_A |
| Organism: | Homo sapiens, Nothocricetulus migratorius |
| Method: | XRD |
| Resolution (Å): | 2.70 |
| Reference: | 10.1073/pnas.1008832107 |
| Antibody | |
| Antibody: | JMJD6 Fab |
| Antibody mutation: | No |
| INN (Clinical Trial): | |
| Antigen | |
| Antigen: | Bifunctional arginine demethylase and lysyl-hydroxylase JMJD6 |
| Antigen mutation: | No |
| Durg Target: | |
Sequence information
Antibody
Heavy Chain: C
Mutation: NULL
| >3LD8_C|Chain C|antibody Fab fragment heavy chain|Cricetulus migratorius (3122392) QIQLQESGPGLVTPSQSLTLTCSVTGDSITSYHWSWIRQFPGKKLEWMGYIYNSGGTDYNPSLKSRVSITREISRNQLFLQLNSVTTEDTATYYCARRDYGTYYFDYWGQGTMVTVSSATTTAPSVYPLAPACDSTTSTTNTVTLGCLVKGYFPEPVTVSWNSGALTSGVHTFPSVLHSGLYSLSSSVTVPSSTWPSQTVTCNVAHPASSTKVDKKIVPGD |
Light Chain: B
Mutation: NULL
| >3LD8_B|Chain B|antibody Fab fragment light chain|Cricetulus migratorius (3122392) DIVMTQSPSSLAVSAGEKVTMSCRSSQSLYYSGIKKNLLAWYQLKPGQSPKLLIYYASTLFTGVPDRFTGSGSGTDYTLTITSVQAEDMGQYFCQQGISNPYTFGAGTKLEIKRADAKPTVSIFPPSSEQLGTGSATLVCFVNNFYPKDINVKWKVDGSEKRDGVLQSVTDQDSKDSTYSLSSTLSLTKADYERHNLYTCEVTHKTSTAAIVKTLNRNEC |
Antigen
Chain: A
Mutation: NULL
| >3LD8_A|Chain A|Bifunctional arginine demethylase and lysyl-hydroxylase JMJD6|Homo sapiens (9606) MNHKSKKRIREAKRSARPELKDSLDWTRHNYYESFSLSPAAVADNVERADALQLSVEEFVERYERPYKPVVLLNAQEGWSAQEKWTLERLKRKYRNQKFKCGEDNDGYSVKMKMKYYIEYMESTRDDSPLYIFDSSYGEHPKRRKLLEDYKVPKFFTDDLFQYAGEKRRPPYRWFVMGPPRSGTGIHIDPLGTSAWNALVQGHKRWCLFPTSTPRELIKVTRDEGGNQQDEAITWFNVIYPRTQLPTWPPEFKPLEILQKPGETVFVPGGWWHVVLNLDTTIAITQNFASSTNFPVVWHKTVRGRPKLSRKWYRILKQEHPELAVLADSVDLQE |
Interaction
1、Solvent accessible surface areas (SASA) were calculated (Naccess V2.1.1) for each residue in antibody and antigen, respectively. The residues with SASA loss in binding of more than 1Å2 were classified as interacting residues.
Interacting residues (ΔSASA based)
| B: SER26 SER28 TYR30 TYR31 SER32 GLY33 LYS35 ASN37 LEU38 SER73 GLY74 GLY97 ILE98 SER99 ASN100 TYR102 C: HIS33 TYR52 ASN53 SER54 GLY56 THR57 ASP58 ARG98 TYR100 GLY101 TYR103 A: GLN53 LEU54 SER55 VAL56 GLU57 GLU58 VAL60 GLU61 ARG62 ARG65 LYS154 ASP158 LEU160 TYR163 SER291 GLU319 HIS320 GLU322 LEU323 VAL325 LEU326 GLN333 |
2、We defined interacting paratope-epitope residues by a distance cutoff of < 5Å . Two amino acids are considered as interacting residues if they have at least one atom within a distance of 5 Å from any atom.
Interacting residues (Atom distance based)
