MolNFT v1 · #124101 · protein
Structure of the C2221 form of PNOB8-like parb-N domain
5K5D · Parb domain protein nuclease: “Structure of the C2221 form of PNOB8-like parb-N domain”. X-ray diffraction, 8 pockets (best druggability 0.73). MolNFT v1 #124101 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5K5D
- Type
- protein
- Length
- 751 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Parb domain protein nuclease
- UniProt
- D0KSP7
- Pockets
- 8 · best druggability 0.73
Structure
x-ray diffraction · 3 distinct chains · 54% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Parb domain protein nuclease | protein | 250 | 55% helix, 12% strand | D0KSP7 |
| A | Parb domain protein nuclease | protein | 252 | 54% helix, 12% strand | D0KSP7 |
| C | Parb domain protein nuclease | protein | 249 | 54% helix, 11% strand | D0KSP7 |
Ligands and binding sites
- CIT · Citric acid · additive · 4 copies · chains B, A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 846 | 0.73 | 0.78 | 80 | CIT |
| 2 | 329 | 0.65 | 0.80 | 38 | CIT |
| 3 | 224 | 0.60 | 0.81 | 33 | CIT |
| 4 | 117 | 0.43 | 0.77 | 15 | empty |
| 5 | 76 | 0.39 | 0.78 | 15 | empty |
Interfaces
1 interface between chains.
- B–A · 639 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 21 modified (engineered).
Compared structures
- 5K5D · Structure of the C2221 form of Pnob8-like ParB-N domain · the same entry in another collection · chain B against B, 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 D0KSP7
- Elsewhere: RCSB PDB 5K5D · PDBe 5K5D · UniProt D0KSP7
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