SMTL ID : 9fzc.1 (1 other biounit)

Structure of OmpA-short in complex with nanobody Nb01

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.27 Å

Oligo State

hetero-1-1-mer

Ligands

6 x OCT: N-OCTANE(Non-covalent)

OCT.1: 8 residues within 4Å: Chain A: L.15, G.16, W.17, N.35, Q.36, L.37, L.166 Ligands: OCT.2 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:W.17, A:L.37 OCT.2: 3 residues within 4Å: Chain A: W.17, N.35 Ligands: OCT.1 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:W.17 OCT.3: 2 residues within 4Å: Chain A: A.13, A.41 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:A.41 OCT.4: 8 residues within 4Å: Chain A: T.11, A.41, F.42, G.43, M.55, G.56, Y.57, V.79 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:A.41, A:V.79 OCT.5: 6 residues within 4Å: Chain A: F.125, A.126, G.127, Y.143, Q.144, W.145 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:Y.143, A:Y.143, A:W.145 OCT.6: 5 residues within 4Å: Chain A: A.39, Y.57, W.59, K.75, Q.77 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:W.59

1 x CA: CALCIUM ION(Non-covalent)

CA.7: 3 residues within 4Å: Chain A: N.147, N.148, D.160 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.160, A:D.160, H2O.1, H2O.1, H2O.2

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sorgenfrei, M. et al., Rapid detection and capture of clinical Escherichia coli strains mediated by OmpA-targeting nanobodies. To Be Published

Release Date

2024-07-17

Peptides

Outer membrane protein A: A
Nanobody 01: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

Membrane

We predict this structure to be a membrane protein.
Show / Hide

Outer membrane protein A

Nanobody 01

Related Entries With Identical Sequence