Research workbench
Crystal structure of a pyrrolidone-carboxylate peptidase 1 (target id nysgrc-012831) from xenorhabdus bovienii ss-2004
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
- 4GXH
- Type
- protein
- Length
- 814 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
- PO4, CL
- Pockets
- 7 · best druggability 0.66
Structure
x-ray diffraction · 3 distinct chains · 35% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Pyrrolidone-carboxylate peptidase (EC 3.4.19.3) | protein | 202 | 36% helix, 24% strand | D3V0W1 |
| B | Pyrrolidone-carboxylate peptidase (EC 3.4.19.3) | protein | 205 | 35% helix, 26% strand | D3V0W1 |
| D | Pyrrolidone-carboxylate peptidase (EC 3.4.19.3) | protein | 205 | 35% helix, 25% strand | D3V0W1 |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 5 copies · chains A, B, C, D
- CL · Chloride ion · ion · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 629 | 0.66 | 0.76 | 74 | CL |
| 2 | 308 | 0.57 | 0.77 | 38 | CL |
| 3 | 234 | 0.55 | 0.78 | 31 | CL |
| 4 | 118 | 0.38 | 0.74 | 25 | empty |
| 5 | 78 | 0.35 | 0.76 | 11 | empty |
Interfaces
4 interfaces between chains.
- A–B · 689 Ų buried · 5 hydrogen bonds · protein-protein
- C–D · 675 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 654 Ų buried · 9 hydrogen bonds · protein-protein
- A–D · 652 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 21 modified (engineered).
Compared structures
- 4GXH · 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 4GXH · PDBe 4GXH · UniProt D3V0W1
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