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The crystal structure of a putative nicotinate-nucleotide adenylyltransferase from vibrio parahaemolyticus
Analyse The crystal structure of a putative nicotinate-nucleotide adenylyltransferase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3H05
- Type
- protein
- Length
- 318 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uncharacterized protein VPA0413
- UniProt
- Q87J40
- Ligands
- CL
- Pockets
- 3 · best druggability 0.51
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Uncharacterized protein VPA0413 | protein | 155 | 46% helix, 17% strand | Q87J40 |
| B | Uncharacterized protein VPA0413 | protein | 163 | 44% helix, 17% strand | Q87J40 |
Ligands and binding sites
- CL · Chloride ion · ion · 2 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 231 | 0.51 | 0.76 | 36 | CL |
| 2 | 159 | 0.42 | 0.74 | 30 | CL |
| 3 | 72 | 0.37 | 0.78 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 1055 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 3H05 · The Crystal Structure of a Putative Nicotinate-nucleotide Adenylyltransferase from Vibrio… · 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 Q87J40
- Elsewhere: RCSB PDB 3H05 · PDBe 3H05 · UniProt Q87J40
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