SMTL ID : 5j1x.4 (3 other biounits)

X-ray structure of neuropilin-1 b1 domain complexed with Arg-5 ligand.

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

monomer

Ligands

1 x AR5: N~2~-(tert-butoxycarbonyl)-L-arginine(Non-covalent)

AR5.1: 10 residues within 4Å: Chain A: Y.28, W.32, T.47, D.51, S.77, T.80, K.82, Y.84, G.145, I.146 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:Y.28, A:W.32, A:T.80 Hydrogen bonds: A:S.77, A:E.79, A:T.80, A:I.146, A:I.146 Water bridges: A:T.47, A:T.47 Salt bridges: A:D.51

1 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.2: 4 residues within 4Å: Chain A: Y.53, A.140, T.141, W.142 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:W.142 pi-Cation interactions: A:W.142, A:W.142

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mota, F. et al., Architecture and hydration of the arginine-binding site of neuropilin-1. FEBS J. (2018)

Release Date

2017-04-05

Peptides

Neuropilin-1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

Neuropilin-1

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