Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 6741 |
| PDBID: | 3WKM |
| Chains: | IM_B |
| Organism: | Aquifex aeolicus VF5, Mus musculus |
| Method: | XRD |
| Resolution (Å): | 2.20 |
| Reference: | 10.1016/j.str.2013.12.003 |
| Antibody | |
| Antibody: | 3WKM Fab |
| Antibody mutation: | No |
| INN (Clinical Trial): | |
| Antigen | |
| Antigen: | The PSD-95/Dlg/ZO-1 tandem of Aquifex aeolicus intramembrane protease RseP(AaPDZ tandem) |
| Antigen mutation: | No |
| Durg Target: | |
Sequence information
Antibody
Heavy Chain: I
Mutation: NULL
| >3WKM_I|Chain B[auth H], E[auth I]|MOUSE IGG1-KAPPA FAB (HEAVY CHAIN)|MUS MUSCULUS (10090) EVQLQQSGAELVKPGASVKLSCTASGFNIKDTYLHWVKQRPEHGLEWIGRIDPANGNAKYDPKFQDKATITADTSSNTAYLQLNSLTSEDTAVYYCSNRQLGLRGYYYAMDYWGQGTSVSVSSAKTTPPSVYPLAPGSAAQTNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVPSSTWPSETVTCNVAHPASSTKVDKKIVPRDC |
Light Chain: M
Mutation: NULL
| >3WKM_M|Chain C[auth L], F[auth M]|MOUSE IGG1-KAPPA FAB (LIGHT CHAIN)|MUS MUSCULUS (10090) YIVLTQSPVSLAVSLGQRATISCRASESVDSYGDSFMHWYQQKPGQPPKLLIYLASNLESGVPARFSGSGSRTDFTLTIDPVEADDAATYYCQQNNEDPWTFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC |
Antigen
Chain: B
Mutation: NULL
| >3WKM_B|Chain A, D[auth B]|Putative zinc metalloprotease aq_1964|Aquifex aeolicus (224324) GSEVPKYLKEPVVVGYVQRDSIAQKIGIKPGDKIIKINGYEVRTWEDLRDALIRLSLDGVKETTLFLERNGEVLHLTIKVPNVQKGEELGIAPLVKPVVGGVKKGSPADQVGIKPGDLILEVNGKKINTWYELVEEVRKSQGKAIKLKILRNGKMIEKELIPAKDPKTGTYFIGLFPKTE |
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)
| I: GLU1 LYS30 ASP31 THR32 TYR33 HIS35 ARG50 ASP52 ALA54 ARG99 GLN100 LEU101 LEU103 ARG104 GLY105 TYR106 TYR107 TYR108 MET110 M: SER31 TYR32 PHE36 SER56 ASN57 LEU58 GLU59 SER60 GLY61 VAL62 PRO63 ALA64 GLY68 SER69 GLY70 SER71 ASN95 ASN96 TRP100 B: GLY113 SER114 GLU115 VAL116 PRO117 TYR119 ARG161 ASP162 ILE165 LEU169 VAL195 LYS197 GLY198 GLU200 VAL207 VAL214 LYS215 LYS216 TRP242 TYR243 VAL246 ARG250 GLN253 LYS276 PRO278 LYS279 THR280 GLY281 THR282 TYR283 PHE284 LEU287 PHE288 PRO289 THR291 |
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)
