Research workbench
Structure of oligopeptidase B from leishmania major
Analyse Structure of oligopeptidase B from leishmania major in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2XE4
- Type
- protein
- Length
- 724 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Oligopeptidase B; Antipain
- EC
- 3.4.21.83
- UniProt
- Q4QHU7
- Ligands
- FC0, NA, CL, PO4
- Pockets
- 7 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 21% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Oligopeptidase B (EC 3.4.21.83) | protein | 721 | 21% helix, 31% strand | Q4QHU7 |
| B | Antipain | protein | 3 | 0% helix, 0% strand | — |
Ligands and binding sites
- FC0 · N-carboxy-L-phenylalanine · ligand · chains A, B
- NA · Sodium ion · metal · 2 copies · chains A
- CL · Chloride ion · ion · 4 copies · chains A
- PO4 · Phosphate ion · ion · 3 copies · chains A, B
- PGR · R-1,2-propanediol · additive · 48 copies · chains A
- GOL · Glycerol · additive · 10 copies · chains A
- PGO · S-1,2-propanediol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 858 | 0.76 | 0.79 | 69 | PGR, CL |
| 2 | 396 | 0.70 | 0.82 | 36 | GOL, PGR, PGO, PO4 |
| 3 | 531 | 0.69 | 0.79 | 54 | FC0, PGR |
| 4 | 96 | 0.56 | 0.85 | 27 | PGR |
| 5 | 128 | 0.43 | 0.76 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 480 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent, 1 modified (covalent ligand, nonstandard).
Compared structures
- 2XE4 · Structure of Oligopeptidase B from Leishmania major · the same entry in another collection · chain B against B, 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 Q4QHU7
- Elsewhere: RCSB PDB 2XE4 · PDBe 2XE4 · UniProt Q4QHU7
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