SMTL ID : 4cth.1

Neprilysin variant G399V,G714K in complex with phosphoramidon

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.15 Å

Oligo State

homo-dimer

Ligands

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

NAG.1: 3 residues within 4Å: Chain A: N.104, A.107, D.464 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.104 NAG.2: 4 residues within 4Å: Chain A: T.142, K.145, N.284, E.288 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.284, A:E.288, A:E.288 NAG.3: 4 residues within 4Å: Chain A: Y.583, G.586, N.587 Ligands: GOL.6 No protein-ligand interaction detected (PLIP) NAG.14: 3 residues within 4Å: Chain B: N.104, A.107, D.464 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.104 NAG.15: 4 residues within 4Å: Chain B: T.142, K.145, N.284, E.288 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.284, B:E.288 NAG.16: 4 residues within 4Å: Chain B: Y.583, G.586, N.587 Ligands: GOL.19 No protein-ligand interaction detected (PLIP)

2 x ZN: ZINC ION(Non-covalent)

ZN.4: 4 residues within 4Å: Chain A: H.543, H.547, E.606 Ligands: RDF.13 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:H.543, A:H.547, A:E.606, A:E.606, RDF.13 ZN.17: 4 residues within 4Å: Chain B: H.543, H.547, E.606 Ligands: RDF.26 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Ligand interactions Metal complexes: B:H.543, B:H.547, B:E.606, B:E.606, RDF.26

16 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 6 residues within 4Å: Chain A: F.504, Y.505, E.544, H.547, E.606 Ligands: RDF.13 Ligand excluded by PLIP GOL.6: 7 residues within 4Å: Chain A: V.582, G.586, L.598, N.599, G.600, I.601 Ligands: NAG.3 Ligand excluded by PLIP GOL.7: 8 residues within 4Å: Chain A: N.380, P.442, D.444, I.445, K.451, D.492, E.493, W.494 Ligand excluded by PLIP GOL.8: 8 residues within 4Å: Chain A: C.102, I.108, S.340, S.341, K.347, T.366, R.369, Y.466 Ligand excluded by PLIP GOL.9: 6 residues within 4Å: Chain A: E.37, C.39, H.693, C.694, R.695, S.698 Ligand excluded by PLIP GOL.10: 5 residues within 4Å: Chain A: L.214, Q.217, E.218, T.345, Y.346 Ligand excluded by PLIP GOL.11: 4 residues within 4Å: Chain A: P.121, D.122, Y.124, Q.149 Ligand excluded by PLIP GOL.12: 4 residues within 4Å: Chain A: R.407, L.433, I.435, E.437 Ligand excluded by PLIP GOL.18: 6 residues within 4Å: Chain B: F.504, Y.505, E.544, H.547, E.606 Ligands: RDF.26 Ligand excluded by PLIP GOL.19: 7 residues within 4Å: Chain B: V.582, G.586, L.598, N.599, G.600, I.601 Ligands: NAG.16 Ligand excluded by PLIP GOL.20: 8 residues within 4Å: Chain B: N.380, P.442, D.444, I.445, K.451, D.492, E.493, W.494 Ligand excluded by PLIP GOL.21: 8 residues within 4Å: Chain B: C.102, I.108, S.340, S.341, K.347, T.366, R.369, Y.466 Ligand excluded by PLIP GOL.22: 6 residues within 4Å: Chain B: E.37, C.39, H.693, C.694, R.695, S.698 Ligand excluded by PLIP GOL.23: 5 residues within 4Å: Chain B: L.214, Q.217, E.218, T.345, Y.346 Ligand excluded by PLIP GOL.24: 4 residues within 4Å: Chain B: P.121, D.122, Y.124, Q.149 Ligand excluded by PLIP GOL.25: 4 residues within 4Å: Chain B: R.407, L.433, I.435, E.437 Ligand excluded by PLIP

2 x RDF: N-ALPHA-L-RHAMNOPYRANOSYLOXY(HYDROXYPHOSPHINYL)-L-LEUCYL-L-TRYPTOPHAN(Non-covalent)

RDF.13: 19 residues within 4Å: Chain A: F.66, V.501, N.502, A.503, F.504, I.518, F.523, V.540, H.543, E.544, H.547, E.606, V.652, W.653, V.670, H.671, R.677 Ligands: ZN.4, GOL.5 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:F.66, A:V.501, A:I.518, A:F.523, A:W.653, A:W.653, A:V.670 Hydrogen bonds: A:V.501, A:N.502, A:N.502, A:N.502, A:N.502, A:R.677, A:R.677 Salt bridges: A:H.671, A:H.671 RDF.26: 19 residues within 4Å: Chain B: F.66, V.501, N.502, A.503, F.504, I.518, F.523, V.540, H.543, E.544, H.547, E.606, V.652, W.653, V.670, H.671, R.677 Ligands: ZN.17, GOL.18 16 PLIP interactions: 16 interactions with chain B Hydrophobic interactions: B:F.66, B:V.501, B:I.518, B:F.523, B:W.653, B:W.653, B:V.670 Hydrogen bonds: B:V.501, B:N.502, B:N.502, B:N.502, B:N.502, B:R.677, B:R.677 Salt bridges: B:H.671, B:H.671

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Webster, C.I. et al., Engineering Neprilysin Activity and Specificity to Create a Novel Therapeutic for Alzheimer'S Disease. Plos One (2014)

Release Date

2014-08-13

Peptides

NEPRILYSIN: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

NEPRILYSIN