Research workbench
Crystal structure of a nipsnap family protein with unknown function (ATU4242) from agrobacterium tumefaciens str. C58 at 1.50 a resolution
Analyse Crystal structure of a nipsnap family protein with unknown function (ATU4242)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1VQS
- Type
- protein
- Length
- 551 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hypothetical protein AGR_L_1239
- UniProt
- Q8U857
- Ligands
- SO4
- Pockets
- 7 · best druggability 0.41
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D, E | Hypothetical protein AGR_L_1239 | protein | 110 | 39% helix, 34% strand | Q8U857 |
| B | Hypothetical protein AGR_L_1239 | protein | 111 | 36% helix, 34% strand | Q8U857 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 5 copies · chains A, B, C, D, E
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 2 copies · chains B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 77 | 0.41 | 0.79 | 16 | empty |
| 2 | 81 | 0.41 | 0.79 | 20 | empty |
| 3 | 84 | 0.41 | 0.78 | 17 | empty |
| 4 | 54 | 0.41 | 0.81 | 19 | empty |
| 5 | 65 | 0.40 | 0.79 | 19 | empty |
Interfaces
4 interfaces between chains.
- C–D · 1726 Ų buried · 24 hydrogen bonds · protein-protein
- A–B · 1682 Ų buried · 22 hydrogen bonds · protein-protein
- D–E · 222 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 218 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 20 modified (engineered).
Compared structures
- 1VQS · Crystal structure of a nipsnap family protein with unknown function (atu4242) 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 Q8U857
- Elsewhere: RCSB PDB 1VQS · PDBe 1VQS · UniProt Q8U857
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