Research workbench
Structure of human neurolysin (E475Q) in complex with neurotensin peptide products
Analyse Structure of human neurolysin (E475Q) in complex with neurotensin peptide… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5LUZ
- Type
- protein
- Length
- 1,342 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Neurolysin, mitochondrial; Pro-arg-arg-pro neurotensin fragment
- EC
- 3.4.24.16
- UniProt
- Q9BYT8
- Ligands
- ZN, CL
- Pockets
- 18 · best druggability 0.90
Structure
x-ray diffraction · 5 distinct chains · 59% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Neurolysin, mitochondrial (EC 3.4.24.16) | protein | 662 | 59% helix, 7% strand | Q9BYT8 |
| B | Neurolysin, mitochondrial (EC 3.4.24.16) | protein | 665 | 60% helix, 7% strand | Q9BYT8 |
| C | Pro-arg-arg-pro neurotensin fragment | protein | 4 | 0% helix, 25% strand | — |
| D | Pro-arg-arg-pro neurotensin fragment | protein | 5 | 0% helix, 20% strand | — |
| P, Q | Pro-arg-arg-pro neurotensin fragment | protein | 3 | 0% helix, 0% strand | — |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 copies · chains A, C, B, D
- CL · Chloride ion · ion · 2 copies · chains A, B
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1084 | 0.90 | 0.91 | 123 | empty |
| 2 | 1135 | 0.86 | 0.87 | 101 | empty |
| 3 | 905 | 0.85 | 0.87 | 88 | empty |
| 4 | 69 | 0.72 | 0.97 | 25 | empty |
| 5 | 743 | 0.71 | 0.77 | 60 | empty |
Interfaces
7 interfaces between chains.
- A–B · 805 Ų buried · 20 hydrogen bonds · protein-protein
- B–D · 611 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 469 Ų buried · 4 hydrogen bonds · protein-protein
- B–Q · 450 Ų buried · 7 hydrogen bonds · protein-protein
- A–P · 425 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 5LUZ · Structure of Human Neurolysin (E475Q) in complex with neurotensin peptide products · the same entry in another collection · chain Q against Q, TM-score 1.00
- Q9BYT8 · AlphaFold monomer V2.0 prediction for neurolysin, mitochondrial (Q9BYT8) · a predicted model of the same protein · chain A against A, TM-score 0.98
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt Q9BYT8
- Elsewhere: RCSB PDB 5LUZ · PDBe 5LUZ · UniProt Q9BYT8
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