Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 1402 |
| PDBID: | 5HGG |
| Chains: | S_B |
| Organism: | Homo sapiens, Vicugna pacos |
| Method: | XRD |
| Resolution (Å): | 1.97 |
| Reference: | 10.1074/jbc.M116.732503 |
| Antibody | |
| Antibody: | Nb4 Nanobody |
| Antibody mutation: | No |
| INN (Clinical Trial): | |
| Antigen | |
| Antigen: | Urokinase-type plasminogen activator |
| Antigen mutation: | No |
| Durg Target: | P00749 |
Sequence information
Antibody
Chain: S
Mutation: NULL
| >5HGG_S|Chain C[auth S], D[auth T]|Camelid Derived Antibody Fragment, Nb4|Vicugna pacos (30538) QVQLQESGGGLVQAGGSLRLSCAASGFTLDSYAIGWFRQAPGKEREGVSCISASGGSTNYADSVKGRFTISRDNAKNTVYLQMNSLKSEDTAVYYCAADHPGLCTSESGRRRYLEVWGQGTQVTVSSA |
Antigen
Chain: B
Mutation: NULL
| >5HGG_B|Chain A, B|Urokinase-type plasminogen activator|Homo sapiens (9606) IIGGEFTTIENQPWFAAIYRRHRGGSVTYVCGGSLISPCWVISATHCFIDYPKKEDYIVYLGRSRLNSNTQGEMKFEVENLILHKDYSADTLAHHNDIALLKIRSKEGRCAQPSRTIQTIALPSMYNDPQFGTSCEITGFGKEQSTDYLYPEQLKMTVVKLISHRECQQPHYYGSEVTTKMLCAADPQWKTDSCQGDSGGPLVCSLQGRMTLTGIVSWGRGCALKDKPGVYTRVSHFLPWIRSHTK |
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 S: GLN1 VAL2 GLY26 PHE27 THR28 SER31 TYR32 ALA53 PRO101 THR105 SER106 GLU107 SER108 GLY109 ARG110 ARG111 ARG112 TYR113 LEU114 GLU115 B: ARG35 SER37 THR39 TYR40 VAL41 CYS42 HIS57 CYS58 LEU73 ALA96 LEU97 HIS99 LYS143 TYR149 TYR151 ASP189 SER190 CYS191 GLN192 GLY193 SER195 VAL213 SER214 TRP215 GLY216 ARG217 GLY219 CYS220 LYS224 GLY226 |
2、We defined interacting paratope-epitope residues by a distance cutoff of < 6 Å . Two amino acids are considered as interacting residues if they have at least one atom within a distance of 6 Å from any atom.
Interacting residues (Atom distance based)
