MolNFT v1 · #77741 · protein
Crystal structure of bacillus amyloliquefaciens pyroglutamyl peptidase I
3RNZ · Pyrrolidone-carboxylate peptidase: “Crystal structure of bacillus amyloliquefaciens pyroglutamyl peptidase I”. X-ray diffraction, 6 pockets (best druggability 0.69). MolNFT v1 #77741 on GenesisL1: 3D structure, binding sites and…
- PDB
- 3RNZ
- Type
- protein
- Length
- 828 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
- P46107
- Pockets
- 6 · best druggability 0.69
Structure
x-ray diffraction · 3 distinct chains · 32% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pyrrolidone-carboxylate peptidase (EC 3.4.19.3) | protein | 207 | 33% helix, 23% strand | P46107 |
| B | Pyrrolidone-carboxylate peptidase (EC 3.4.19.3) | protein | 209 | 32% helix, 23% strand | P46107 |
| C, D | Pyrrolidone-carboxylate peptidase (EC 3.4.19.3) | protein | 206 | 33% helix, 23% strand | P46107 |
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 901 | 0.69 | 0.75 | 86 | empty |
| 2 | 467 | 0.62 | 0.76 | 49 | empty |
| 3 | 378 | 0.58 | 0.75 | 44 | empty |
| 4 | 77 | 0.32 | 0.75 | 23 | empty |
| 5 | 80 | 0.31 | 0.74 | 18 | empty |
Interfaces
4 interfaces between chains.
- C–D · 742 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 728 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 692 Ų buried · 4 hydrogen bonds · protein-protein
- A–D · 692 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 3RNZ · Crystal structure of Bacillus Amyloliquefaciens Pyroglutamyl Peptidase I · the same entry in another collection · chain A against A, TM-score 1.00
- P46107 · AlphaFold monomer V2.0 prediction for pyrrolidone-carboxylate peptidase (P46107) · 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 P46107
- Elsewhere: RCSB PDB 3RNZ · PDBe 3RNZ · UniProt P46107
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