MolNFT v1 · #55905 · protein
Crystal structure of the proline iminopeptidase-related protein TTHA1809 from thermus thermophilus HB8
2YYS: “Crystal structure of the proline iminopeptidase-related protein TTHA1809 from thermus thermophilus HB8”. X-ray diffraction, 5 pockets (best druggability 0.71). MolNFT v1 #55905 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 2YYS
- Type
- protein
- Length
- 564 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Proline iminopeptidase-related protein
- UniProt
- Q5SHC1
- Pockets
- 5 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 44% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Proline iminopeptidase-related protein | protein | 284 | 44% helix, 17% strand | Q5SHC1 |
| B | Proline iminopeptidase-related protein | protein | 280 | 43% helix, 18% strand | Q5SHC1 |
Ligands and binding sites
- GOL · Glycerol · additive · 6 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 373 | 0.71 | 0.83 | 57 | GOL |
| 2 | 622 | 0.71 | 0.78 | 48 | GOL |
| 3 | 537 | 0.68 | 0.78 | 39 | GOL |
| 4 | 113 | 0.50 | 0.81 | 24 | empty |
| 5 | 63 | 0.27 | 0.73 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 904 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 2YYS · Crystal structure of the proline iminopeptidase-related protein TTHA1809 from Thermus… · 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 Q5SHC1
- Elsewhere: RCSB PDB 2YYS · PDBe 2YYS · UniProt Q5SHC1
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