Research workbench
Crystal structure of bacillus amyloliquefaciens pyroglutamyl peptidase I and terpyridine PLATINUM(II)
Analyse Crystal structure of bacillus amyloliquefaciens pyroglutamyl peptidase I and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3RO0
- Type
- protein
- Length
- 829 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
- Ligands
- TPT
- Pockets
- 6 · best druggability 0.70
Structure
x-ray diffraction · 4 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 | 32% helix, 23% strand | P46107 |
| B | Pyrrolidone-carboxylate peptidase (EC 3.4.19.3) | protein | 209 | 32% helix, 23% strand | P46107 |
| C | Pyrrolidone-carboxylate peptidase (EC 3.4.19.3) | protein | 207 | 32% helix, 23% strand | P46107 |
| D | Pyrrolidone-carboxylate peptidase (EC 3.4.19.3) | protein | 206 | 33% helix, 23% strand | P46107 |
Ligands and binding sites
- TPT · 2,2':6',2''-TERPYRIDINE PLATINUM(II) Chloride · ligand · 5 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
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 | 880 | 0.70 | 0.75 | 85 | TPT |
| 2 | 455 | 0.62 | 0.76 | 46 | TPT |
| 3 | 460 | 0.62 | 0.76 | 47 | TPT |
| 4 | 85 | 0.33 | 0.74 | 18 | empty |
| 5 | 80 | 0.32 | 0.74 | 22 | empty |
Interfaces
4 interfaces between chains.
- C–D · 727 Ų buried · 2 hydrogen bonds · protein-protein
- A–B · 724 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 687 Ų buried · 4 hydrogen bonds · protein-protein
- A–D · 687 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 3RO0 · Crystal structure of Bacillus amyloliquefaciens pyroglutamyl peptidase I and terpyridine… · the same entry in another collection · chain D against D, 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 3RO0 · PDBe 3RO0 · UniProt P46107
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