MolNFT v1 · #57824 · protein
Crystal structure of L-3-hydroxynorvaline bound L-threonine dehydrogenase (Y137F) from hyperthermophilic archaeon thermoplasma volcanium
3AJR · Ndp-sugar epimerase: “Crystal structure of L-3-hydroxynorvaline bound L-threonine dehydrogenase (Y137F) from hyperthermophilic…”. X-ray diffraction, 2 ligands (VAH, NAD), 3 pockets (best druggability 0.77). MolNFT v1 #57824 on…
- PDB
- 3AJR
- Type
- protein
- Length
- 622 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ndp-sugar epimerase
- EC
- 1.1.1.103
- UniProt
- Q97BK3
- Ligands
- VAH, NAD
- Pockets
- 3 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ndp-sugar epimerase (EC 1.1.1.103) | protein | 314 | 44% helix, 16% strand | Q97BK3 |
| B | Ndp-sugar epimerase (EC 1.1.1.103) | protein | 308 | 45% helix, 17% strand | Q97BK3 |
Ligands and binding sites
- VAH · (3R)-3-hydroxy-L-norvaline · ligand · 2 copies · chains A, B
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 2 copies · chains A, B
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 434 | 0.77 | 0.86 | 49 | VAH, NAD |
| 2 | 436 | 0.77 | 0.86 | 49 | VAH, NAD |
| 3 | 50 | 0.26 | 0.73 | 10 | MPD |
Interfaces
1 interface between chains.
- A–B · 1377 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 3AJR · Crystal structure of L-3-Hydroxynorvaline bound L-Threonine dehydrogenase (Y137F) from… · the same entry in another collection · chain B against B, 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
- Every structure of UniProt Q97BK3
- Elsewhere: RCSB PDB 3AJR · PDBe 3AJR · UniProt Q97BK3
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