MolNFT v1 · #50169 · protein
Crystal structure of putative dinucleotide-binding oxidoreductase (NP_786167.1) from lactobacillus plantarum at 1.60 a resolution
2RAF: “Crystal structure of putative dinucleotide-binding oxidoreductase (NP_786167.1) from lactobacillus plantarum…”. X-ray diffraction, 1 ligand (NAP), 4 pockets (best druggability 0.78). MolNFT v1 #50169 on GenesisL1: 3D structure…
- PDB
- 2RAF
- Type
- protein
- Length
- 587 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative dinucleotide-binding oxidoreductase
- EC
- 1.-.-.-
- UniProt
- Q88TW8
- Ligands
- NAP
- Pockets
- 4 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 35% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Putative dinucleotide-binding oxidoreductase (EC 1.-.-.-) | protein | 190 | 36% helix, 24% strand | Q88TW8 |
| B | Putative dinucleotide-binding oxidoreductase (EC 1.-.-.-) | protein | 207 | 34% helix, 26% strand | Q88TW8 |
Ligands and binding sites
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · chains A
- PEG · Di(hydroxyethyl)ether · additive · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1032 | 0.78 | 0.80 | 70 | PEG |
| 2 | 175 | 0.49 | 0.77 | 25 | NAP |
| 3 | 175 | 0.48 | 0.76 | 26 | empty |
| 4 | 53 | 0.37 | 0.80 | 14 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1604 Ų buried · 35 hydrogen bonds · protein-protein
- B–C · 537 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 modified (engineered).
Compared structures
- 2RAF · Crystal structure of putative dinucleotide-binding oxidoreductase (NP_786167.1) from… · 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
- Every structure of UniProt Q88TW8
- Elsewhere: RCSB PDB 2RAF · PDBe 2RAF · UniProt Q88TW8
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