Research workbench
Crystal structure of pron-tk-sp from thermococcus kodakaraensis
Analyse Crystal structure of pron-tk-sp from thermococcus kodakaraensis in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3AFG
- Type
- protein
- Length
- 1,012 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Subtilisin-like serine protease
- EC
- 3.4.21.62
- UniProt
- Q5JIZ5
- Ligands
- CA
- Pockets
- 10 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 22% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Subtilisin-like serine protease (EC 3.4.21.62) | protein | 505 | 22% helix, 32% strand | Q5JIZ5 |
| B | Subtilisin-like serine protease (EC 3.4.21.62) | protein | 507 | 21% helix, 33% strand | Q5JIZ5 |
Ligands and binding sites
- CA · Calcium ion · metal · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 836 | 0.74 | 0.78 | 93 | empty |
| 2 | 221 | 0.59 | 0.80 | 26 | empty |
| 3 | 229 | 0.53 | 0.77 | 20 | empty |
| 4 | 152 | 0.47 | 0.77 | 18 | empty |
| 5 | 133 | 0.45 | 0.77 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 651 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 3AFG · Crystal structure of ProN-Tk-SP from Thermococcus kodakaraensis · the same entry in another collection · chain A against A, TM-score 1.00
- Q5JIZ5 · AlphaFold monomer V2.0 prediction for subtilisin-like serine protease (Q5JIZ5) · a predicted model of the same protein · chain B 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 Q5JIZ5
- Elsewhere: RCSB PDB 3AFG · PDBe 3AFG · UniProt Q5JIZ5
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