Research workbench
Crystal structure of TM0922, a fusion of a domain of unknown function and ADP/ATP-dependent NAD(P)H-hydrate dehydratase from thermotoga maritima in complex with ATP
Analyse Crystal structure of TM0922, a fusion of a domain of unknown function and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3RRF
- Type
- protein
- Length
- 496 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative uncharacterized protein; Peptide
- EC
- 4.2.1.93
- UniProt
- Q9X024
- Ligands
- ATP, K, MG
- Pockets
- 4 · best druggability 0.62
Structure
x-ray diffraction · 2 distinct chains · 45% 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 | Peptide | protein | 7 | 0% helix, 29% strand | — |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 2 copies · chains A
- K · Potassium ion · metal · chains A
- MG · Magnesium ion · metal · chains A
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 230 | 0.62 | 0.82 | 33 | ATP, GOL |
| 2 | 337 | 0.58 | 0.76 | 41 | empty |
| 3 | 220 | 0.52 | 0.77 | 38 | MG, ATP |
| 4 | 72 | 0.31 | 0.74 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 362 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 3RRF · 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 3RRF · PDBe 3RRF · UniProt Q9X024
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