Research workbench
Crystal structure of a protein with unknown function from DUF364 family (PH1506) from pyrococcus horikoshii at 2.70 a resolution
Analyse Crystal structure of a protein with unknown function from DUF364 family… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3NPG
- Type
- protein
- Length
- 980 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uncharacterized DUF364 family protein
- UniProt
- O59175
- Pockets
- 4 · best druggability 0.89
Structure
x-ray diffraction · 4 distinct chains · 40% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Uncharacterized DUF364 family protein | protein | 249 | 42% helix, 23% strand | O59175 |
| B | Uncharacterized DUF364 family protein | protein | 240 | 39% helix, 24% strand | O59175 |
| C | Uncharacterized DUF364 family protein | protein | 246 | 40% helix, 24% strand | O59175 |
| D | Uncharacterized DUF364 family protein | protein | 245 | 39% helix, 23% strand | O59175 |
Ligands and binding sites
- ACT · Acetate ion · additive · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 969 | 0.89 | 0.90 | 148 | ACT |
| 2 | 614 | 0.80 | 0.85 | 76 | ACT |
| 3 | 82 | 0.72 | 0.96 | 16 | empty |
| 4 | 79 | 0.45 | 0.81 | 18 | empty |
Interfaces
6 interfaces between chains.
- A–C · 1296 Ų buried · 28 hydrogen bonds · protein-protein
- B–D · 1207 Ų buried · 26 hydrogen bonds · protein-protein
- A–B · 1163 Ų buried · 18 hydrogen bonds · protein-protein
- C–D · 1151 Ų buried · 23 hydrogen bonds · protein-protein
- B–C · 245 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 29 modified (engineered).
Compared structures
- 3NPG · Crystal structure of a protein with unknown function from DUF364 family (PH1506) from… · 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 O59175
- Elsewhere: RCSB PDB 3NPG · PDBe 3NPG · UniProt O59175
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