Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 706 |
| PDBID: | 4CKD |
| Chains: | IM_D |
| Organism: | Escherichia coli K-12, Mus musculus |
| Method: | EM |
| Resolution (Å): | 13.00 |
| Reference: | 10.1016/j.str.2014.01.011 |
| Antibody | |
| Antibody: | 13R4 Fv |
| Antibody mutation: | No |
| INN (Clinical Trial): | |
| Antigen | |
| Antigen: | Escherichia coli β-galactosidase |
| Antigen mutation: | No |
| Durg Target: | P00722 |
Sequence information
Antibody
Heavy Chain: I
Mutation: NULL
| >4CKD_I|Chain E[auth H], F[auth I], G[auth J], H[auth K]|SCFV13R4 ANTIBODY FV HEAVY CHAIN|MUS MUSCULUS (10090) DVQLQESGPSLVKPSQTLSLTCSVTGDSITSDYWSWIRKFPGNRLEYMGYVSYSGSTYYNPSLKSRISITRDTSKNQYYLDLNSVTTEDTATYYCANWDGDYWGQGTLVTVSAA |
Light Chain: M
Mutation: NULL
| >4CKD_M|Chain I[auth L], J[auth M], K[auth N], L[auth O]|SCFV13R4 ANTIBODY FV LIGHT CHAIN|MUS MUSCULUS (10090) DIVLTQSPATLSVTPGNSVSLSCRASQSIGNDLHWYQQKSHESPRLLIKYASQSISGIPSRFSGSGSGTDFTLSINSVETEDFGMYFCQQSNSWPYTFGGGTKLEIK |
Antigen
Chain: D
Mutation: NULL
| >4CKD_D|Chain A, B, C, D|BETA-GALACTOSIDASE|ESCHERICHIA COLI K-12 (83333) MTMITDSLAVVLQRRDWENPGVTQLNRLAAHPPFASWRNSEEARTDRPSQQLRSLNGEWRFAWFPAPEAVPESWLECDLPEADTVVVPSNWQMHGYDAPIYTNVTYPITVNPPFVPTENPTGCYSLTFNVDESWLQEGQTRIIFDGVNSAFHLWCNGRWVGYGQDSRLPSEFDLSAFLRAGENRLAVMVLRWSDGSYLEDQDMWRMSGIFRDVSLLHKPTTQISDFHVATRFNDDFSRAVLEAEVQMCGELRDYLRVTVSLWQGETQVASGTAPFGGEIIDERGGYADRVTLRLNVENPKLWSAEIPNLYRAVVELHTADGTLIEAEACDVGFREVRIENGLLLLNGKPLLIRGVNRHEHHPLHGQVMDEQTMVQDILLMKQNNFNAVRCSHYPNHPLWYTLCDRYGLYVVDEANIETHGMVPMNRLTDDPRWLPAMSERVTRMVQRDRNHPSVIIWSLGNESGHGANHDALYRWIKSVDPSRPVQYEGGGADTTATDIICPMYARVDEDQPFPAVPKWSIKKWLSLPGETRPLILCEYAHAMGNSLGGFAKYWQAFRQYPRLQGGFVWDWVDQSLIKYDENGNPWSAYGGDFGDTPNDRQFCMNGLVFADRTPHPALTEAKHQQQFFQFRLSGQTIEVTSEYLFRHSDNELLHWMVALDGKPLASGEVPLDVAPQGKQLIELPELPQPESAGQLWLTVRVVQPNATAWSEAGHISAWQQWRLAENLSVTLPAASHAIPHLTTSEMDFCIELGNKRWQFNRQSGFLSQMWIGDKKQLLTPLRDQFTRAPLDNDIGVSEATRIDPNAWVERWKAAGHYQAEAALLQCTADTLADAVLITTAHAWQHQGKTLFISRKTYRIDGSGQMAITVDVEVASDTPHPARIGLNCQLAQVAERVNWLGLGPQENYPDRLTAACFDRWDLPLSDMYTPYVFPSENGLRCGTRELNYGPHQWRGDFQFNISRYSQQQLMETSHRHLLHAEEGTWLNIDGFHMGIGGDDSWSPSVSAEFQLSAGRYHYQLVWCQK |
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)
| Chain residues position delta_SASA
: residuesposition I: ASP1 SER28 THR30 SER31 ASP32 TYR33 TYR50 SER52 TYR53 SER54 SER56 TYR58 ARG71 ASP72 THR73 SER74 ASN76 TRP98 ASP99 TYR102 M: GLN27 SER28 GLY30 ASN31 ASP32 HIS34 LYS49 TYR50 SER52 GLN53 SER54 SER56 GLY64 SER65 SER91 ASN92 SER93 TRP94 D: ARG46 PRO47 SER53 ASN55 GLY56 GLU57 THR83 VAL85 MET92 HIS360 PRO361 LEU362 HIS363 ASP368 GLU369 GLN370 VAL373 GLN374 LEU377 LEU397 TYR405 SER574 ILE576 TYR578 GLU580 ASN581 GLY582 ASN583 PRO584 TRP585 SER586 PHE608 ALA609 ASP610 ARG611 THR612 ALA705 THR706 ALA707 GLU710 ARG973 |
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)
