MolNFT v1 · #50385 · protein
Crystal structure of a protein of unknown function with a cystatin- like fold (NPUN_R3134) from nostoc punctiforme pcc 73102 at 1.80 a resolution
2RGQ · Domain of unknown function with a cystatin-like fold: “Crystal structure of a protein of unknown function with a cystatin- like fold (NPUN_R3134) from nostoc…”. X-ray diffraction, 1 ligand (K), 5 pockets (best druggability 0.88).…
- PDB
- 2RGQ
- Type
- protein
- Length
- 401 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Domain of unknown function with a cystatin-like fold
- Ligands
- K
- Pockets
- 5 · best druggability 0.88
Structure
x-ray diffraction · 2 distinct chains · 31% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Domain of unknown function with a cystatin-like fold | protein | 133 | 31% helix, 47% strand | — |
| B, C | Domain of unknown function with a cystatin-like fold | protein | 134 | 31% helix, 46% strand | — |
Ligands and binding sites
- K · Potassium ion · metal · chains A, B, C
- GOL · Glycerol · additive · 5 copies · chains A, B, C
- PEG · Di(hydroxyethyl)ether · additive · chains 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 405 | 0.88 | 0.96 | 59 | K |
| 2 | 208 | 0.73 | 0.89 | 38 | empty |
| 3 | 62 | 0.71 | 0.96 | 19 | empty |
| 4 | 81 | 0.67 | 0.92 | 25 | empty |
| 5 | 73 | 0.28 | 0.72 | 19 | empty |
Interfaces
3 interfaces between chains.
- B–C · 934 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 920 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 919 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 15 modified (engineered).
Compared structures
- 2RGQ · Crystal structure of a protein of unknown function with a cystatin-like fold (npun_r3134)… · 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
- Elsewhere: RCSB PDB 2RGQ · PDBe 2RGQ
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