SMTL ID : 6gid.1

High resolution crystal structure of substrate-free human neprilysin

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

monomer

Ligands

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

NAG.1: 3 residues within 4Å: Chain A: N.91, A.94, D.451 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.91 NAG.2: 4 residues within 4Å: Chain A: T.129, N.271, N.274, E.275 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:N.274 Hydrogen bonds: A:N.271, A:E.275 NAG.3: 4 residues within 4Å: Chain A: Y.570, G.573, N.574, K.691 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.574, A:K.691, A:K.691 NAG.4: 2 residues within 4Å: Chain A: N.231, K.300 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.231, A:K.300 Water bridges: A:N.231, A:N.231

1 x ZN: ZINC ION(Non-covalent)

ZN.5: 5 residues within 4Å: Chain A: H.530, H.534, E.593, H.658 Ligands: PO4.18 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.530, A:H.534, A:E.593, A:E.593

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

EDO.6: 5 residues within 4Å: Chain A: G.142, K.143, K.144, R.169, R.320 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.142, A:K.143, A:K.144, A:R.320 EDO.7: 4 residues within 4Å: Chain A: F.150, G.152, T.153, Y.293 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.153 Water bridges: A:Y.293 EDO.8: 6 residues within 4Å: Chain A: R.203, P.209, I.210, D.211, Q.214, L.215 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.211 Water bridges: A:Q.214 EDO.9: 2 residues within 4Å: Chain A: R.239, L.245 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.239 Water bridges: A:R.239 EDO.10: 3 residues within 4Å: Chain A: A.391, R.394, E.395 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.395 Water bridges: A:A.391 EDO.11: 2 residues within 4Å: Chain A: I.482, F.491 No protein-ligand interaction detected (PLIP)

2 x NO3: NITRATE ION(Non-functional Binders)

NO3.12: 7 residues within 4Å: Chain A: V.145, L.146, P.168, R.169, E.226, I.229, R.320 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.146, A:R.320 NO3.13: 7 residues within 4Å: Chain A: N.338, R.341, K.342, T.347, T.348, S.349, E.350 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.348 Water bridges: A:N.338, A:R.341, A:T.347

3 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.14: 4 residues within 4Å: Chain A: P.108, D.109, Y.111, Y.124 No protein-ligand interaction detected (PLIP) PEG.15: 2 residues within 4Å: Chain A: S.48, Y.648 1 PLIP interactions: 1 interactions with chain A Water bridges: A:R.341 PEG.16: 8 residues within 4Å: Chain A: F.53, N.489, H.530, E.531, W.640, H.658, R.664 Ligands: PO4.18 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.664, A:R.664

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.17: 4 residues within 4Å: Chain A: E.121, Q.214, E.218, R.311 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.121, A:E.218

1 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.18: 9 residues within 4Å: Chain A: N.489, A.490, H.530, E.531, H.534, E.593, H.658 Ligands: ZN.5, PEG.16 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:A.490, A:E.593 Water bridges: A:E.531 Salt bridges: A:H.530, A:H.534, A:H.658

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Moss, S. et al., High resolution crystal structure of substrate-free human neprilysin. J. Struct. Biol. (2018)

Release Date

2018-06-27

Peptides

Neprilysin: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Neprilysin

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