SMTL ID : 8vjv.1

Structure of Human Neurolysin in complex with dynorphin A8(1-8) peptide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.12 Å

Oligo State

monomer

Ligands

1 x TYR- GLY- GLY- PHE- ARG- ARG: Dynorphin A(1-8)(Non-covalent)

TYR-GLY-GLY-PHE-ARG-ARG.1: 28 residues within 4Å: Chain A: N.166, F.231, N.232, R.234, Y.409, H.411, A.412, A.413, C.414, T.457, H.460, E.461, H.464, E.489, Q.493, E.496, R.540, Q.541, L.544, T.584, H.587, G.590, Y.592, Y.596, Y.599, L.600, E.603 Ligands: ZN.2 22 PLIP interactions: 22 interactions with chain A Hydrophobic interactions: A:Y.409, A:A.413, A:T.457, A:L.544, A:Y.599 Hydrogen bonds: A:N.166, A:R.234, A:C.414, A:E.461, A:Q.493, A:R.540, A:T.584, A:T.584, A:T.584, A:G.590, A:Y.596, A:Y.596, A:Y.599 Water bridges: A:L.600, A:L.600 Salt bridges: A:E.603 pi-Stacking: A:H.460

1 x ZN: ZINC ION(Non-covalent)

ZN.2: 6 residues within 4Å: Chain A: H.460, H.464, E.489, S.492 Ligands: TYR-GLY-GLY-PHE-ARG-ARG.1, TYR-GLY-GLY-PHE-ARG-ARG.1 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.460, A:H.464, A:E.489, A:E.489

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

EDO.3: 6 residues within 4Å: Chain A: W.13, D.14, L.15, P.72, V.81, W.377 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.15, A:L.15 EDO.4: 4 residues within 4Å: Chain A: Y.346, H.511, D.514, S.516 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.514, A:S.516 EDO.5: 4 residues within 4Å: Chain A: Y.211, E.228, N.232, A.321 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.232

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.6: 2 residues within 4Å: Chain A: N.149, K.152 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Shi, K. et al., Structural basis of divergent substrate recognition and inhibition of human neurolysin. Sci Rep (2024)

Release Date

2024-08-21

Peptides

Neurolysin, mitochondrial: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Neurolysin, mitochondrial

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