SMTL ID : 4gz9.2 (1 other biounit)

Mouse Neuropilin-1, extracellular domains 1-4 (a1a2b1b2)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

homo-dimer

Ligands

2 x NAG- NAG- BMA: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA.1: 3 residues within 4Å: Chain A: N.132, I.158, F.160 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.10: 3 residues within 4Å: Chain B: N.132, I.158, F.160 No protein-ligand interaction detected (PLIP)

2 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.2: 5 residues within 4Å: Chain A: I.168, E.170, N.243, Y.244, S.245 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.170 NAG.11: 5 residues within 4Å: Chain B: I.168, E.170, N.243, Y.244, S.245 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.170

4 x CA: CALCIUM ION(Non-covalent)

CA.3: 5 residues within 4Å: Chain A: E.177, D.191, D.232, A.234, I.235 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.177, A:D.191, A:A.234, A:I.235, H2O.2 CA.4: 5 residues within 4Å: Chain A: E.60, D.67, D.108, E.110, T.111 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.60, A:D.67, A:D.108, A:T.111, H2O.2 CA.12: 5 residues within 4Å: Chain B: E.177, D.191, D.232, A.234, I.235 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.177, B:D.191, B:A.234, B:I.235, H2O.3 CA.13: 5 residues within 4Å: Chain B: E.60, D.67, D.108, E.110, T.111 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.60, B:D.67, B:D.108, B:T.111, H2O.3

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

SO4.5: 6 residues within 4Å: Chain A: R.219, L.261, E.267, I.268, L.312, R.316 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:L.261, A:E.267 Salt bridges: A:R.219, A:R.316 SO4.6: 3 residues within 4Å: Chain A: N.464, W.466, R.545 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.464, A:N.464 Salt bridges: A:R.545 SO4.14: 6 residues within 4Å: Chain B: R.219, L.261, E.267, I.268, L.312, R.316 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:L.261 Salt bridges: B:R.219, B:R.316 SO4.15: 3 residues within 4Å: Chain B: N.464, W.466, R.545 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.464, B:N.464 Salt bridges: B:R.545

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

EDO.7: 4 residues within 4Å: Chain A: K.148, N.151, I.235, A.236 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.148, A:N.151 EDO.8: 2 residues within 4Å: Chain A: R.219, G.313 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.219 EDO.9: 5 residues within 4Å: Chain A: K.355, I.361, F.377, S.378, L.381 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.378 EDO.16: 4 residues within 4Å: Chain B: K.148, N.151, I.235, A.236 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.148, B:N.151 EDO.17: 2 residues within 4Å: Chain B: R.219, G.313 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.219 EDO.18: 5 residues within 4Å: Chain B: K.355, I.361, F.377, S.378, L.381 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.378

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Janssen, B.J.C. et al., Neuropilins lock secreted semaphorins onto plexins in a ternary signaling complex. Nat.Struct.Mol.Biol. (2012)

Release Date

2012-10-17

Peptides

Neuropilin-1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Neuropilin-1

Related Entries With Identical Sequence