Research workbench
Crystal structure of NAD+ synthetase from burkholderia pseudomallei
Analyse Crystal structure of NAD+ synthetase from burkholderia pseudomallei in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3DPI
- Type
- protein
- Length
- 499 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NAD+ synthetase
- Pockets
- 4 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 59% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | NAD+ synthetase | protein | 269 | 58% helix, 7% strand | — |
| B | NAD+ synthetase | protein | 230 | 59% helix, 9% strand | — |
Ligands and binding sites
- ACT · Acetate ion · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 826 | 0.79 | 0.82 | 90 | empty |
| 2 | 183 | 0.43 | 0.74 | 28 | empty |
| 3 | 88 | 0.41 | 0.78 | 13 | empty |
| 4 | 52 | 0.40 | 0.82 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 1466 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 3DPI · Crystal Structure of NAD+ synthetase from Burkholderia Pseudomallei · 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
- Elsewhere: RCSB PDB 3DPI · PDBe 3DPI
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