SMTL ID : 6tdb.1 (3 other biounits)

Neuropilin2-b1 domain in a complex with the C-terminal VEGFB167 peptide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.45 Å

Oligo State

monomer

Ligands

1 x ARG- LYS- LEU- ARG- ARG: C-terminal VEGFB167 peptide(Non-covalent)

ARG-LYS-LEU-ARG-ARG.1: 13 residues within 4Å: Chain A: Y.28, D.30, R.32, W.33, T.48, D.52, S.78, E.80, T.81, Y.85, G.146, I.147 Ligands: ACE.3 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:Y.28, A:W.33, A:T.81 Hydrogen bonds: A:T.48, A:S.78 Water bridges: A:Y.28, A:D.30, A:W.33 Salt bridges: A:D.30, A:D.52 pi-Cation interactions: A:W.33, A:Y.85

1 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.2: 5 residues within 4Å: Chain A: K.111, V.112, F.113, Q.114, N.125 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.111, A:Q.114

1 x ACE: ACETYL GROUP(Non-functional Binders)

ACE.3: 2 residues within 4Å: Ligands: ARG-LYS-LEU-ARG-ARG.1, ARG-LYS-LEU-ARG-ARG.1 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Eldrid, C. et al., NRP2-b1 domain in a complex with the C-terminal VEGFB167 peptide. To Be Published

Release Date

2020-11-18

Peptides

Neuropilin-2: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Neuropilin-2

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