Research workbench
Thermostable phosphite dehydrogenase A176R variant in complex with NAD
Analyse Thermostable phosphite dehydrogenase A176R variant in complex with NAD in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4E5P
- Type
- protein
- Length
- 1,969 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thermostable phosphite dehydrogenase A176R variant
- Ligands
- NAD
- Pockets
- 19 · best druggability 0.78
Structure
x-ray diffraction · 5 distinct chains · 36% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Thermostable phosphite dehydrogenase A176R variant | protein | 332 | 35% helix, 17% strand | — |
| B | Thermostable phosphite dehydrogenase A176R variant | protein | 331 | 36% helix, 17% strand | — |
| C, D | Thermostable phosphite dehydrogenase A176R variant | protein | 325 | 36% helix, 17% strand | — |
| E | Thermostable phosphite dehydrogenase A176R variant | protein | 328 | 36% helix, 17% strand | — |
| F | Thermostable phosphite dehydrogenase A176R variant | protein | 328 | 35% helix, 17% strand | — |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 6 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 922 | 0.78 | 0.80 | 109 | NAD |
| 2 | 880 | 0.77 | 0.80 | 99 | NAD |
| 3 | 1190 | 0.76 | 0.78 | 132 | NAD |
| 4 | 664 | 0.74 | 0.80 | 66 | NAD |
| 5 | 458 | 0.72 | 0.82 | 52 | NAD |
Interfaces
9 interfaces between chains.
- B–D · 2893 Ų buried · 35 hydrogen bonds · protein-protein
- A–C · 2878 Ų buried · 33 hydrogen bonds · protein-protein
- E–F · 2813 Ų buried · 27 hydrogen bonds · protein-protein
- A–F · 666 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 657 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 4E5P · Thermostable phosphite dehydrogenase A176R variant 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 4E5P · PDBe 4E5P
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