Research workbench
Crystal structure of a ntf-2 like protein of unknown function (SPO1084) from silicibacter pomeroyi dss-3 at 1.69 a resolution
Analyse Crystal structure of a ntf-2 like protein of unknown function (SPO1084) from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3FKA
- Type
- protein
- Length
- 477 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uncharacterized ntf-2 like protein
- UniProt
- Q5LUH0
- Ligands
- UNL
- Pockets
- 3 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 33% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D | Uncharacterized ntf-2 like protein | protein | 119 | 33% helix, 50% strand | Q5LUH0 |
| B | Uncharacterized ntf-2 like protein | protein | 120 | 33% helix, 49% strand | Q5LUH0 |
Ligands and binding sites
- UNL · Unknown ligand · ligand · 9 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 7 copies · chains A, B, C, D
- ACT · Acetate ion · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 130 | 0.75 | 0.95 | 41 | empty |
| 2 | 67 | 0.62 | 0.90 | 17 | UNL |
| 3 | 60 | 0.33 | 0.77 | 15 | empty |
Interfaces
6 interfaces between chains.
- A–B · 1399 Ų buried · 9 hydrogen bonds · protein-protein
- C–D · 1365 Ų buried · 10 hydrogen bonds · protein-protein
- A–D · 601 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 589 Ų buried · 7 hydrogen bonds · protein-protein
- B–D · 39 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 24 modified (engineered).
Compared structures
- 3FKA · Crystal structure of a ntf-2 like protein of unknown function (SPO1084) from silicibacter… · 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 Q5LUH0
- Elsewhere: RCSB PDB 3FKA · PDBe 3FKA · UniProt Q5LUH0
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.