MolNFT v1 · #77924 · protein
Crystal structure of TM0922, a fusion of a domain of unknown function and ADP/ATP-dependent NAD(P)H-hydrate dehydratase from thermotoga maritima soaked with NADH and ADP.
3RTD · Putative uncharacterized protein: “Crystal structure of TM0922, a fusion of a domain of unknown function and ADP/ATP-dependent NAD(P)H-hydrate…”. X-ray diffraction, 5 ligands (NAI, ADP, NAX), 3 pockets (best druggability 0.67).…
- PDB
- 3RTD
- Type
- protein
- Length
- 496 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative uncharacterized protein; Unknown peptide, probably from expression host
- EC
- 4.2.1.93
- UniProt
- Q9X024
- Ligands
- NAI, ADP, NAX, K, MG
- Pockets
- 3 · best druggability 0.67
Structure
x-ray diffraction · 2 distinct chains · 46% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative uncharacterized protein (EC 4.2.1.93) | protein | 489 | 46% helix, 16% strand | Q9X024 |
| B | Unknown peptide, probably from expression host | protein | 7 | 0% helix, 29% strand | — |
Ligands and binding sites
- NAI · 1,4-dihydronicotinamide adenine dinucleotide · ligand · chains A
- ADP · Adenosine-5'-diphosphate · ligand · chains A
- NAX · Beta-6-hydroxy-1,4,5,6-tetrhydronicotinamide adenine dinucleotide · ligand · chains A
- K · Potassium ion · metal · chains A
- MG · Magnesium ion · metal · chains A
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 | 523 | 0.67 | 0.78 | 62 | NAI |
| 2 | 226 | 0.54 | 0.77 | 32 | MG, ADP |
| 3 | 148 | 0.47 | 0.77 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 362 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 3RTD · Crystal structure of tm0922, a fusion of a domain of unknown function and… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9X024 · AlphaFold monomer V2.0 prediction for bifunctional NAD(P)H-hydrate repair enzyme nnr… · a predicted model of the same protein · chain A against A, TM-score 0.99
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 Q9X024
- Elsewhere: RCSB PDB 3RTD · PDBe 3RTD · UniProt Q9X024
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