MolNFT v1 · #89988 · protein
Thermostable phosphite dehydrogenase in complex with NAD and sulfite
4E5K · Phosphite dehydrogenase (thermostable variant): “Thermostable phosphite dehydrogenase in complex with NAD and sulfite”. X-ray diffraction, 2 ligands (NAD, SO3), 9 pockets (best druggability 0.79). MolNFT v1 #89988 on GenesisL1: 3D…
- PDB
- 4E5K
- Type
- protein
- Length
- 1,315 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phosphite dehydrogenase (thermostable variant)
- Ligands
- NAD, SO3
- Pockets
- 9 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 36% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D | Phosphite dehydrogenase (thermostable variant) | protein | 329 | 37% helix, 17% strand | — |
| C | Phosphite dehydrogenase (thermostable variant) | protein | 328 | 35% helix, 16% strand | — |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 4 copies · chains A, B, C, D
- SO3 · Sulfite ion · ion · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 980 | 0.79 | 0.81 | 110 | NAD, SO3 |
| 2 | 234 | 0.66 | 0.83 | 36 | NAD, SO3 |
| 3 | 244 | 0.65 | 0.82 | 40 | SO3, NAD |
| 4 | 217 | 0.64 | 0.83 | 36 | NAD, SO3 |
| 5 | 302 | 0.54 | 0.75 | 41 | empty |
Interfaces
5 interfaces between chains.
- A–D · 2799 Ų buried · 30 hydrogen bonds · protein-protein
- A–B · 392 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 335 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 242 Ų buried · 5 hydrogen bonds · protein-protein
- B–D · 13 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4E5K · Thermostable phosphite dehydrogenase in complex with NAD and sulfite · 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 4E5K · PDBe 4E5K
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