SMTL ID : 6tjt.1 (1 other biounit)

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.31 Å

Oligo State

monomer

Ligands

1 x ILE- ARG- ARG: VEGFC C terminal peptide(Non-covalent)

ILE-ARG-ARG.1: 10 residues within 4Å: Chain A: Y.28, W.33, T.48, D.52, S.78, E.80, T.81, Y.85, G.146, I.147 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:Y.28, A:S.78, A:E.80, A:E.80, A:Y.85, A:I.147 Water bridges: A:W.33, A:W.33, A:T.48, A:T.48, A:E.80 Salt bridges: A:D.52

2 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 4 residues within 4Å: Chain A: G.84, Y.86, D.118, A.119 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.84, A:A.119 Water bridges: A:Y.86, A:T.120 SO4.3: 3 residues within 4Å: Chain A: H.110, K.111, V.112 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.111, A:V.112 Water bridges: A:H.110, A:H.110 Salt bridges: A:H.110

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

EDO.4: 5 residues within 4Å: Chain A: N.7, A.70, L.124, K.126, F.154 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 VEGFC peptide. To Be Published

Release Date

2020-12-16

Peptides

Neuropilin-2: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Neuropilin-2

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