Research workbench
X-ray crystalline structures of pyrrolidone carboxyl peptidase from a hyperthermophile, pyrococcus furiosus, and its cys-free mutant
Analyse X-ray crystalline structures of pyrrolidone carboxyl peptidase from a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1IOF
- Type
- protein
- Length
- 832 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
- O73944
- Pockets
- 4 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain · 36% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Pyrrolidone carboxyl peptidase (EC 3.4.19.3) | protein | 208 | 36% helix, 23% strand | O73944 |
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 952 | 0.74 | 0.78 | 71 | empty |
| 2 | 475 | 0.66 | 0.78 | 33 | empty |
| 3 | 475 | 0.64 | 0.77 | 35 | empty |
| 4 | 53 | 0.40 | 0.81 | 16 | empty |
Interfaces
6 interfaces between chains.
- B–D · 709 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 696 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 648 Ų buried · 10 hydrogen bonds · protein-protein
- A–D · 646 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 126 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 1IOF · X-ray crystalline structures of pyrrolidone carboxyl peptidase from a hyperthermophile… · the same entry in another collection · chain A against A, TM-score 1.00
- O73944 · AlphaFold monomer V2.0 prediction for pyrrolidone-carboxylate peptidase (O73944) · a predicted model of the same protein · 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 O73944
- Elsewhere: RCSB PDB 1IOF · PDBe 1IOF · UniProt O73944
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