SMTL ID : 4qdq.1 (1 other biounit)

Physical basis for Nrp2 ligand binding

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

homo-dimer

Ligands

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 5 residues within 4Å: Chain A: K.276, F.278, E.279, R.290, R.291 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:K.276, A:E.279, A:R.291 Water bridges: A:I.289, A:I.289, A:R.291 GOL.2: 3 residues within 4Å: Chain A: N.83, G.84, H.144 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.83, A:G.84, A:H.144 GOL.3: 6 residues within 4Å: Chain A: W.101, M.102, V.103, R.105, H.110, H.283 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:V.103, A:R.105, A:H.110, A:H.283 GOL.5: 5 residues within 4Å: Chain B: K.276, F.278, E.279, R.290, R.291 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:K.276, B:E.279, B:R.291 Water bridges: B:I.289, B:I.289, B:R.291 GOL.6: 3 residues within 4Å: Chain B: N.83, G.84, H.144 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.83, B:G.84, B:H.144 GOL.7: 6 residues within 4Å: Chain B: W.101, M.102, V.103, R.105, H.110, H.283 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:V.103, B:R.105, B:H.110, B:H.283

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

SO4.4: 3 residues within 4Å: Chain A: H.41, Q.74, R.150 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.74 Salt bridges: A:H.41, A:R.150 SO4.8: 3 residues within 4Å: Chain B: H.41, Q.74, R.150 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.74 Salt bridges: B:H.41, B:R.150

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Parker, M.W. et al., Structural Basis for VEGF-C Binding to Neuropilin-2 and Sequestration by a Soluble Splice Form. Structure (2015)

Release Date

2015-04-15

Peptides

Neuropilin-2: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Neuropilin-2

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