MolNFT v1 · #105836 · protein
Crystal structure of recombinant prolidase from thermococcus sibiricus at P21221 spacegroup
4RGZ · Xaa-pro aminopeptidase: “Crystal structure of recombinant prolidase from thermococcus sibiricus at P21221 spacegroup”. X-ray diffraction, 2 ligands (ZN, PO4), 20 pockets (best druggability 0.83). MolNFT v1 #105836 on GenesisL1: 3D…
- PDB
- 4RGZ
- Type
- protein
- Length
- 1,468 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Xaa-pro aminopeptidase
- UniProt
- C6A2N7
- Ligands
- ZN, PO4
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 1 distinct chain · 28% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, N, 1, e | Xaa-pro aminopeptidase | protein | 367 | 28% helix, 20% strand | C6A2N7 |
Ligands and binding sites
- ZN · Zinc ion · metal · 8 copies · chains A, N, 1, e
- PO4 · Phosphate ion · ion · 3 copies · chains 1, e
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1083 | 0.83 | 0.84 | 117 | ZN |
| 2 | 432 | 0.75 | 0.84 | 59 | empty |
| 3 | 264 | 0.75 | 0.88 | 48 | ZN |
| 4 | 821 | 0.74 | 0.79 | 81 | empty |
| 5 | 58 | 0.67 | 0.95 | 15 | empty |
Interfaces
4 interfaces between chains.
- 1–e · 2137 Ų buried · 26 hydrogen bonds · protein-protein
- A–N · 1913 Ų buried · 18 hydrogen bonds · protein-protein
- N–1 · 303 Ų buried · 3 hydrogen bonds · protein-protein
- A–1 · 194 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4RGZ · Crystal structure of recombinant prolidase from Thermococcus sibiricus at P21221… · 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 C6A2N7
- Elsewhere: RCSB PDB 4RGZ · PDBe 4RGZ · UniProt C6A2N7
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