SMTL ID : 8vju.1

Structure of Human Neurolysin in complex with dynorphin A13 peptide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.99 Å

Oligo State

hetero-1-1-mer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: H.460, H.464, E.489, S.492 Chain B: R.6 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Metal complexes: A:H.460, A:H.464, A:E.489, A:E.489, B:R.6 ZN.10: 2 residues within 4Å: Chain A: W.601, Q.655 No protein-ligand interaction detected (PLIP)

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

EDO.2: 3 residues within 4Å: Chain A: E.294, R.297 Ligands: EDO.4 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.297 EDO.3: 6 residues within 4Å: Chain A: W.13, D.14, L.15, P.72, S.76, V.81 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.15, A:L.15 EDO.4: 5 residues within 4Å: Chain A: R.297, S.568, E.569, G.572 Ligands: EDO.2 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.297, A:E.569 EDO.5: 1 residues within 4Å: Chain A: Q.244 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.244 EDO.6: 6 residues within 4Å: Chain A: A.321, Y.563, C.567, L.571, V.573, A.574 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.563 Water bridges: A:E.228, A:N.232, A:T.576 EDO.7: 7 residues within 4Å: Chain A: Y.360, L.363, L.364, P.491, M.494, L.495, Y.628 No protein-ligand interaction detected (PLIP) EDO.8: 2 residues within 4Å: Chain A: E.59, R.477 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.59 EDO.9: 6 residues within 4Å: Chain A: T.31, Y.35, Y.62, F.95, D.96, M.99 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.35, A:F.95, A:D.96

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

CL.11: 1 residues within 4Å: Chain A: G.7 Ligand excluded by PLIP

2 x NA: SODIUM ION(Non-functional Binders)

NA.12: 3 residues within 4Å: Chain A: C.613, K.627, F.648 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.627, A:F.648 NA.13: 2 residues within 4Å: Chain A: C.219, R.311 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.311

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
Dynorphin A(1-13): B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

Neurolysin, mitochondrial

Dynorphin A(1-13)

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