MolNFT v1 · #141428 · protein
Artificial L-threonine 3-dehydrogenase designed by ancestral sequence reconstruction.
5Z75: “Artificial L-threonine 3-dehydrogenase designed by ancestral sequence reconstruction.”. X-ray diffraction, 2 ligands (NAD, PO4), 11 pockets (best druggability 0.82). MolNFT v1 #141428 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5Z75
- Type
- protein
- Length
- 1,224 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Artificial L-threonine 3-dehydrogenase
- Ligands
- NAD, PO4
- Pockets
- 11 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 44% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Artificial L-threonine 3-dehydrogenase | protein | 306 | 44% helix, 16% strand | — |
| B, C, D | Artificial L-threonine 3-dehydrogenase | protein | 306 | 44% helix, 16% strand | — |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 3 copies · chains A, B, D
- PO4 · Phosphate ion · ion · 7 copies · chains A, B, C, D
- 2PE · Nonaethylene glycol · additive · 3 copies · chains B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 849 | 0.82 | 0.84 | 115 | empty |
| 2 | 361 | 0.76 | 0.86 | 59 | 2PE |
| 3 | 325 | 0.75 | 0.87 | 42 | NAD, PO4 |
| 4 | 349 | 0.74 | 0.85 | 42 | NAD, PO4 |
| 5 | 345 | 0.73 | 0.84 | 41 | NAD, PO4 |
Interfaces
5 interfaces between chains.
- C–D · 1176 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 1145 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 382 Ų buried · 6 hydrogen bonds · protein-protein
- A–D · 217 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 200 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 5Z75 · Artificial L-threonine 3-dehydrogenase designed by ancestral sequence reconstruction. · 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 5Z75 · PDBe 5Z75
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