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Oligopeptidase B from S. proteomaculans with modified hinge region in complex with N-[(1S)-5-amino-1-(CHLOROACETYL)PENTYL]-4- methylbenzenesulfonamide
Analyse Oligopeptidase B from S. proteomaculans with modified hinge region in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7NE7
- Type
- protein
- Length
- 677 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Oligopeptidase B
- UniProt
- B3VI58
- Ligands
- SPM, TCK
- Pockets
- 11 · best druggability 0.62
Structure
x-ray diffraction · 1 distinct chain · 23% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Oligopeptidase B | protein | 677 | 23% helix, 34% strand | B3VI58 |
Ligands and binding sites
- SPM · Spermine · ligand · 6 copies · chains A
- TCK · N-[(1S)-5-amino-1-(chloroacetyl)pentyl]-4-methylbenzenesulfonamide · ligand · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 395 | 0.62 | 0.78 | 54 | empty |
| 2 | 65 | 0.59 | 0.90 | 17 | TCK |
| 3 | 456 | 0.58 | 0.74 | 50 | SPM |
| 4 | 208 | 0.50 | 0.76 | 30 | empty |
| 5 | 100 | 0.40 | 0.77 | 20 | empty |
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 7NE7 · oligopeptidase B from S. proteomaculans with modified hinge region in complex with… · the same entry in another collection · chain A against A, TM-score 1.00
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 B3VI58
- Elsewhere: RCSB PDB 7NE7 · PDBe 7NE7 · UniProt B3VI58
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