MolNFT v1 · #89991 · protein
Thermostable phosphite dehydrogenase in complex with NAD
4E5N: “Thermostable phosphite dehydrogenase in complex with NAD”. X-ray diffraction, 1 ligand (NAD), 20 pockets (best druggability 0.80). MolNFT v1 #89991 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4E5N
- Type
- protein
- Length
- 2,630 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thermostable phosphite dehydrogenase
- Ligands
- NAD
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · 5 distinct chains · 36% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, H | Thermostable phosphite dehydrogenase | protein | 329 | 36% helix, 16% strand | — |
| C, D | Thermostable phosphite dehydrogenase | protein | 330 | 36% helix, 16% strand | — |
| E | Thermostable phosphite dehydrogenase | protein | 328 | 35% helix, 16% strand | — |
| F | Thermostable phosphite dehydrogenase | protein | 327 | 35% helix, 17% strand | — |
| G | Thermostable phosphite dehydrogenase | protein | 328 | 36% helix, 16% strand | — |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 8 copies · chains A, B, C, D, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1195 | 0.80 | 0.81 | 133 | NAD |
| 2 | 933 | 0.79 | 0.81 | 104 | NAD |
| 3 | 833 | 0.76 | 0.80 | 75 | empty |
| 4 | 1107 | 0.73 | 0.76 | 100 | NAD |
| 5 | 931 | 0.70 | 0.75 | 83 | empty |
Interfaces
15 interfaces between chains.
- B–H · 2795 Ų buried · 29 hydrogen bonds · protein-protein
- D–G · 2601 Ų buried · 29 hydrogen bonds · protein-protein
- A–F · 501 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 399 Ų buried · 0 hydrogen bonds · protein-protein
- B–C · 378 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 4E5N · Thermostable phosphite dehydrogenase in complex with NAD · 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 4E5N · PDBe 4E5N
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