SMTL ID : 9en2.1

Crystal structure of the metalloproteinase enhancer PCPE-1 complexed with nanobodies VHH-H4 and VHH-I5

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

hetero-1-1-1-mer

Ligands

2 x CA: CALCIUM ION(Non-covalent)

CA.1: 5 residues within 4Å: Chain A: E.107, D.115, D.156, G.158, T.159 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.107, A:D.156, A:G.158, A:T.159, H2O.4 CA.2: 6 residues within 4Å: Chain A: E.230, D.238, D.280, S.282, V.283 Chain B: K.99 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.230, A:D.238, A:S.282, A:V.283, H2O.1

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 6 residues within 4Å: Chain A: R.102, W.167 Chain B: F.49, A.121, E.122, Q.123 8 PLIP interactions: 3 interactions with chain A, 5 interactions with chain B Hydrogen bonds: A:R.102, A:R.102, B:S.51, B:E.122, B:Q.123 Water bridges: A:Y.69, B:A.121, B:D.124 GOL.4: 7 residues within 4Å: Chain A: C.235, K.256, F.257 Chain C: T.79, N.80, Y.81, K.86 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain C Water bridges: A:D.232, A:T.233, A:K.256, A:K.256 Hydrogen bonds: C:Y.81, C:Y.81

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lagoutte, P. et al., Mono- and Bi-specific Nanobodies Targeting the CUB Domains of PCPE-1 Reduce the Proteolytic Processing of Fibrillar Procollagens. J.Mol.Biol. (2024)

Release Date

2024-07-03

Peptides

Procollagen C-endopeptidase enhancer 1: A
VHH-H4: B
VHH-I5: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Procollagen C-endopeptidase enhancer 1

VHH-H4

VHH-I5