SMTL ID : 4rn5.1

B1 domain of human Neuropilin-1 with acetate ion in a ligand-binding site

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.73 Å

Oligo State

monomer

Ligands

1 x ACT: ACETATE ION(Non-functional Binders)

ACT.1: 4 residues within 4Å: Chain A: W.32, S.77, T.80, Y.84 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:W.32 Hydrogen bonds: A:S.77, A:T.80, A:Y.84, A:Y.84

2 x ZN: ZINC ION(Non-covalent)

ZN.2: 1 residues within 4Å: Chain A: H.18 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.18, H2O.4 ZN.3: 1 residues within 4Å: Chain A: D.20 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:D.20, H2O.6, H2O.6, H2O.7, H2O.7

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 6 residues within 4Å: Chain A: L.10, E.16, I.17, Q.21, L.61, R.65 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.21, A:Q.21, A:R.65

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Allerston, C.K. et al., Conserved water molecules in a ligand-binding site of neuropilin-1. To be Published

Release Date

2015-10-28

Peptides

Neuropilin-1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Neuropilin-1

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