Research workbench
Crystal structure of a nipsnap family protein (ATU5224) from agrobacterium tumefaciens str. C58 at 2.40 a resolution
Analyse Crystal structure of a nipsnap family protein (ATU5224) from agrobacterium… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1VQY
- Type
- protein
- Length
- 847 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hypothetical protein AGR_PAT_315
- UniProt
- Q8UK99
- Ligands
- PO4
- Pockets
- 12 · best druggability 0.71
Structure
x-ray diffraction · 3 distinct chains · 41% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, F, G, H | Hypothetical protein AGR_PAT_315 | protein | 105 | 41% helix, 36% strand | Q8UK99 |
| B | Hypothetical protein AGR_PAT_315 | protein | 114 | 39% helix, 33% strand | Q8UK99 |
| D, E | Hypothetical protein AGR_PAT_315 | protein | 104 | 42% helix, 37% strand | Q8UK99 |
Ligands and binding sites
- PO4 · Phosphate ion · ion · chains G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 582 | 0.71 | 0.80 | 55 | empty |
| 2 | 545 | 0.71 | 0.80 | 53 | empty |
| 3 | 561 | 0.71 | 0.79 | 56 | empty |
| 4 | 558 | 0.71 | 0.80 | 55 | empty |
| 5 | 596 | 0.71 | 0.79 | 59 | empty |
Interfaces
20 interfaces between chains.
- A–B · 1406 Ų buried · 24 hydrogen bonds · protein-protein
- E–F · 1378 Ų buried · 27 hydrogen bonds · protein-protein
- C–D · 1367 Ų buried · 26 hydrogen bonds · protein-protein
- G–H · 1359 Ų buried · 25 hydrogen bonds · protein-protein
- D–F · 405 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 24 modified (engineered).
Compared structures
- 1VQY · CRYSTAL STRUCTURE OF a NIPSNAP FAMILY PROTEIN (ATU5224) FROM AGROBACTERIUM TUMEFACIENS… · 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 Q8UK99
- Elsewhere: RCSB PDB 1VQY · PDBe 1VQY · UniProt Q8UK99
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