Research workbench
Crystal structure of a pyrrolidone-carboxylate peptidase 1 (target id nysgrc-012831) from xenorhabdus bovienii ss-2004 in space group P21
Analyse Crystal structure of a pyrrolidone-carboxylate peptidase 1 (target id… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4HPS
- Type
- protein
- Length
- 830 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pyrrolidone-carboxylate peptidase
- EC
- 3.4.19.3
- UniProt
- D3V0W1
- Ligands
- CL
- Pockets
- 6 · best druggability 0.69
Structure
x-ray diffraction · 3 distinct chains · 33% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pyrrolidone-carboxylate peptidase (EC 3.4.19.3) | protein | 211 | 33% helix, 24% strand | D3V0W1 |
| B | Pyrrolidone-carboxylate peptidase (EC 3.4.19.3) | protein | 209 | 33% helix, 25% strand | D3V0W1 |
| C, D | Pyrrolidone-carboxylate peptidase (EC 3.4.19.3) | protein | 205 | 33% helix, 24% strand | D3V0W1 |
Ligands and binding sites
- CL · Chloride ion · ion · 15 copies · chains A, B, D, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 852 | 0.69 | 0.75 | 89 | CL |
| 2 | 698 | 0.66 | 0.75 | 86 | CL |
| 3 | 94 | 0.37 | 0.75 | 23 | empty |
| 4 | 89 | 0.36 | 0.75 | 13 | empty |
| 5 | 82 | 0.35 | 0.75 | 17 | empty |
Interfaces
4 interfaces between chains.
- B–D · 711 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 711 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 665 Ų buried · 10 hydrogen bonds · protein-protein
- A–D · 664 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 4HPS · Crystal Structure of a Pyrrolidone-carboxylate peptidase 1 (target ID NYSGRC-012831) from… · 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 D3V0W1
- Elsewhere: RCSB PDB 4HPS · PDBe 4HPS · UniProt D3V0W1
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