Research workbench
Pyrrolidone carboxyl peptidase from thermococcus litoralis
Analyse Pyrrolidone carboxyl peptidase from thermococcus litoralis in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1A2Z
- Type
- protein
- Length
- 880 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pyrrolidone carboxyl peptidase
- EC
- 3.4.19.3
- UniProt
- O07883
- Ligands
- SO4
- Pockets
- 9 · best druggability 0.84
Structure
x-ray diffraction · 1 distinct chain · 34% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Pyrrolidone carboxyl peptidase (EC 3.4.19.3) | protein | 220 | 34% helix, 24% strand | O07883 |
Ligands and binding sites
- SO4 · Sulfate 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
9 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1026 | 0.84 | 0.85 | 82 | empty |
| 2 | 969 | 0.84 | 0.85 | 88 | empty |
| 3 | 102 | 0.35 | 0.74 | 19 | empty |
| 4 | 95 | 0.35 | 0.74 | 22 | empty |
| 5 | 80 | 0.35 | 0.75 | 14 | empty |
Interfaces
6 interfaces between chains.
- A–B · 1099 Ų buried · 14 hydrogen bonds · protein-protein
- C–D · 1071 Ų buried · 19 hydrogen bonds · protein-protein
- A–C · 926 Ų buried · 6 hydrogen bonds · protein-protein
- B–D · 921 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 348 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 1A2Z · Pyrrolidone carboxyl peptidase from thermococcus litoralis · the same entry in another collection · chain A against A, TM-score 1.00
- O07883 · AlphaFold monomer V2.0 prediction for pyrrolidone-carboxylate peptidase (O07883) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 O07883
- Elsewhere: RCSB PDB 1A2Z · PDBe 1A2Z · UniProt O07883
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