Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 1582 |
| PDBID: | 5MP2 |
| Chains: | D_B |
| Organism: | Pseudomonas aeruginosa, Lama glama |
| Method: | XRD |
| Resolution (Å): | 2.90 |
| Reference: | 10.1128/mBio.01185-17 |
| Antibody | |
| Antibody: | VHH04 Nanobody |
| Antibody mutation: | No |
| INN (Clinical Trial): | |
| Antigen | |
| Antigen: | Type II secretion system protein D |
| Antigen mutation: | No |
| Durg Target: | |
Sequence information
Antibody
Chain: D
Mutation: NULL
| >5MP2_D|Chain C, D|Camelid nanobody VHH04|Lama glama (9844) MKYLLPTAAAGLLLLAAQPAMAQVQLVESGGGSVQAGGSLRLSCAASGNTDSSYYMGWFRQGPGKEREGVASIYIRAGIPYYTDSVKGRFTISQDNAKNTIYLQMNSLKPEDTAMYFCAGSVRTTIQPFKGNYYNYWGRGTQVTVSSHHHHHH |
Antigen
Chain: B
Mutation: NULL
| >5MP2_B|Chain A, B|Type II secretion system protein D|Pseudomonas aeruginosa (287) ENSGGNAFVPAGNQQEAHWTINLKDADIREFIDQISEITGETFVVDPRVKGQVSVVSKAQLSLSEVYQLFLSVMSTHGFTVVAQGDQARIVPNAEAKTEAGGGQSAPDRLETRVIQVQQSPVSELIPLIRPLVPQYGHLAAVPSANALIISDRSANIARIEDVIRQLDQKGSHDYSVINLRYGWVMDAAEVLNNAMSRGQAKGAAGAQVIADARTNRLIILGPPQARAKLVQLAQSLDTP |
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 D: TYR33 TYR52 ALA55 ILE57 PRO58 TYR59 TYR60 LYS65 ARG101 THR102 THR103 ILE104 GLN105 PRO106 PHE107 LYS108 TYR111 B: ALA51 HIS52 TRP53 THR54 ILE55 ASN56 LEU57 LYS58 GLU64 GLN68 GLU71 ILE72 VAL90 SER91 LYS92 ALA93 GLN94 GLN150 |
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)
