SMTL ID : 5l73.1

MAM domain of human neuropilin-1

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.24 Å

Oligo State

homo-dimer

Ligands

4 x CA: CALCIUM ION(Non-covalent)

CA.1: 4 residues within 4Å: Chain A: E.24, D.58, N.64, D.169 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.24, A:E.24, A:D.58, A:N.64, H2O.2 CA.2: 2 residues within 4Å: Chain A: D.58 Ligands: BCN.3 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.58, H2O.2, H2O.3 CA.5: 4 residues within 4Å: Chain B: E.24, D.58, N.64, D.169 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.24, B:D.58, B:N.64, B:D.169, H2O.4 CA.6: 3 residues within 4Å: Chain B: D.58, T.60 Ligands: BCN.7 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.58, B:T.60, H2O.4

2 x BCN: BICINE(Non-covalent)

BCN.3: 11 residues within 4Å: Chain A: D.58, H.59, T.60, W.98, W.136, D.169 Chain B: E.138, R.140, N.175, I.177 Ligands: CA.2 7 PLIP interactions: 2 interactions with chain B, 5 interactions with chain A Hydrogen bonds: B:E.138, B:R.140, A:H.59, A:T.60, A:D.169 Water bridges: A:G.61 Salt bridges: A:D.58 BCN.7: 9 residues within 4Å: Chain B: Q.57, D.58, H.59, T.60, W.98, W.136, D.169, D.170 Ligands: CA.6 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:D.58, B:H.59, B:T.60, B:D.169, B:D.169, B:D.170 Salt bridges: B:D.58, B:H.59

1 x TAM: TRIS(HYDROXYETHYL)AMINOMETHANE(Non-covalent)

TAM.4: 5 residues within 4Å: Chain A: S.104, I.129, G.130, H.131, Q.132 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.104, A:I.129, A:H.131, A:Q.132

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yelland, T. et al., Crystal Structure of the Neuropilin-1 MAM Domain: Completing the Neuropilin-1 Ectodomain Picture. Structure (2016)

Release Date

2016-10-26

Peptides

Neuropilin-1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Neuropilin-1