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Crystal structure of ADP/ATP-dependent NAD(P)H-hydrate dehydratase from bacillus subtilis co-crystallized with ATP/MG2+.
Analyse Crystal structure of ADP/ATP-dependent NAD(P)H-hydrate dehydratase from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3RPH
- Type
- protein
- Length
- 277 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ADP/ATP-dependent NAD(P)H-hydrate dehydratase
- EC
- 4.2.1.93
- UniProt
- P94368
- Ligands
- AMP, MG, PO4
- Pockets
- 3 · best druggability 0.51
Structure
x-ray diffraction · 1 distinct chain · 43% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ADP/ATP-dependent NAD(P)H-hydrate dehydratase (EC 4.2.1.93) | protein | 277 | 43% helix, 12% strand | P94368 |
Ligands and binding sites
- AMP · Adenosine monophosphate · ligand · 2 copies · chains A
- MG · Magnesium ion · metal · chains A
- PO4 · Phosphate ion · ion · 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 176 | 0.51 | 0.78 | 33 | MG, AMP, PO4 |
| 2 | 61 | 0.32 | 0.75 | 19 | empty |
| 3 | 62 | 0.31 | 0.75 | 15 | empty |
Compared structures
- 3RPH · Crystal Structure of ADP/ATP-dependent NAD(P)H-hydrate dehydratase from Bacillus subtilis… · the same entry in another collection · chain A against A, TM-score 1.00
- P94368 · AlphaFold monomer V2.0 prediction for ADP-dependent (S)-NAD(P)H-hydrate dehydratase… · 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 P94368
- Elsewhere: RCSB PDB 3RPH · PDBe 3RPH · UniProt P94368
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