Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 3902 |
| PDBID: | 7KDD |
| Chains: | FG_B |
| Organism: | Human herpesvirus 5 strain Towne, Homo sapiens |
| Method: | EM |
| Resolution (Å): | 3.50 |
| Reference: | 10.1126/sciadv.abf3178 |
| Antibody | |
| Antibody: | SM5-1 Fab |
| Antibody mutation: | No |
| INN (Clinical Trial): | |
| Antigen | |
| Antigen: | Human cytomegalovirus (HCMV) envelope glycoprotein B |
| Antigen mutation: | No |
| Durg Target: | |
Sequence information
Antibody
Heavy Chain: F
Mutation: NULL
| >7KDD_F|Chain B[auth D], E[auth F], H|SM5-1 Fab antibody heavy chain|Homo sapiens (9606) QVQLVQSGAEVRKPGASVKVSCKASGYSLKDHYMVWVRQAPGQGLEWMGWINPQSGGTGYGQKFQGRVTMTRDTSTNTAYMILSSLRSDDTAVYFCARDGAKTVSNSGLSLLYYHNRLDAWGQGTMVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCGGGGGAGGGGGHHHHHHGSWSHPQFEK |
Light Chain: G
Mutation: NULL
| >7KDD_G|Chain C[auth E], F[auth G], I|SM5-1 Fab antibody light chain|Homo sapiens (9606) QSVLTQPPSVSAAPGQMVTISCSGSSSNIGKNYVSWYQQLPGAAPKLLIFDNNKRPSGTPDRFSGSKSGTSATLVITGLQTGDEADYYCGTPDRSLSVIFGGGTKVTVLGQPKANPTVTLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADGSPVKAGVETTKPSKQSNNKYAASSYLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAPTECS |
Antigen
Chain: B
Mutation: NULL
| >7KDD_B|Chain A, D[auth B], G[auth C]|Envelope glycoprotein B|Human cytomegalovirus (strain Towne) (10363) MESRIWCLVVCVNLCIVCLGAAVSSSSTRGTSATHSHHSSHTTSAAHSRSGSVSQRVTSSQTVSHGVNETIYNTTLKYGDVVGVNTTKYPYRVCSMAQGTDLIRFERNIVCTSMKPINEDLDEGIMVVYKRNIVAHTFKVRVYQKVLTFRRSYAYIHTTYLLGSNTEYVAPPMWEIHHINSHSQCYSSYSRVIAGTVFVAYHRDSYENKTMQLMPDDYSNTHSTRYVTVKDQWHSRGSTWLYRETCNLNCMVTITTARSKYPYHFFATSTGDVVDISPFYNGTNRNASYFGENADKFFIFPNYTIVSDFGRPNSALETHRLVAFLERADSVISWDIQDEKNVTCQLTFWEASERTIRSEAEDSYHFSSAKMTATFLSKKQEVNMSDSALDCVRDEAINKLQQIFNTSYNQTYEKYGNVSVFETTGGLVVFWQGIKQKSLVELERLANRSSLNLTHNRTKRSTDGNNATHLSNMESVHNLVYAQLQFTYDTLRGYINRALAQIAEAWCVDQRRTLEVFKELSKINPSAILSAIYNKPIAARFMGDVLGLASCVTINQTSVKVLRDMNVKESPGRCYSRPVVIFNFANSSYVQYGQLGEDNEILLGNHRTEECQLPSLKIFIAGNSAYEYVDYLFKRMIDLSSISTVDSMIALDIDPLENTDFRVLELYSQKELRSSNVFDLEEIMREFNSYKQRVKYVEDKVVDPLPPYLKGLDDLMSGLGAAGKAVGVAIGAVGGAVASVVEGVATFLKNPFGAFTIILVAIAVVIIIYLIYTRQRRLCMQPLQNLFPYLVSADGTTVTSGNTKDTSLQAPPSYEESVYNSGRKGPGPPSSDASTAAPPYTNEQAYQMLLALVRLDAEQRAQQNGTDSLDGQTGTQDKGQKPNLLDRLRHRKNGYRHLKDSDEEENV |
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 F: SER55 ALA101 LYS102 SER105 SER107 GLY108 LEU109 SER110 LEU111 LEU112 TYR113 TYR114 ASN116 G: GLY30 LYS31 ASN32 TYR33 ASN52 LYS67 B: ASP120 ARG131 LEU346 GLU359 ALA360 GLU361 ASP362 TYR364 LYS379 GLN380 GLU381 VAL382 ASN383 MET384 ASP386 ALA388 LEU389 GLU422 GLY426 VAL428 |
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)
