SMTL ID : 8qgx.1

Complex between human neutrophil elastase with nanobody NbE201

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

hetero-1-1-mer

Ligands

2 x NAG- NAG- FUC: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-FUC.1: 9 residues within 4Å: Chain A: R.49, A.50, V.51, R.52, V.69, F.70, A.71, N.95, G.96 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:R.52, A:A.71, A:V.69 Hydrogen bonds: A:R.52, A:R.52 NAG-NAG-FUC.2: 10 residues within 4Å: Chain A: R.5, W.12, Q.121, C.122, L.123, N.144, V.178, C.179, N.180, G.181 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:W.12, A:V.178, A:W.12 Hydrogen bonds: A:Q.121, A:N.180, A:G.181

1 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.3: 6 residues within 4Å: Chain A: R.114, L.116, C.179, N.180, L.182, H.184 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.180 Salt bridges: A:R.114, A:H.184

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Redeghieri, P. et al., Enzymatic, structural, and biophysical characterization of a single-domain antibody (VHH) selectively and tightly inhibiting neutrophil elastase and exhibiting favorable developability properties. Protein Sci. (2024)

Release Date

2024-12-25

Peptides

Neutrophil elastase: A
NbE201: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Neutrophil elastase

NbE201

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