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Crystal structure of BPRO0239 oxidoreductase from polaromonas sp. JS666 in NADP bound form
Analyse Crystal structure of BPRO0239 oxidoreductase from polaromonas sp. JS666 in NADP… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4IQG
- Type
- protein
- Length
- 977 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Short-chain DEHYDROGENASE/REDUCTASE sdr
- UniProt
- Q12GY8
- Ligands
- NAP
- Pockets
- 9 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 49% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C, B | Short-chain DEHYDROGENASE/REDUCTASE sdr | protein | 247 | 50% helix, 16% strand | Q12GY8 |
| A | Short-chain DEHYDROGENASE/REDUCTASE sdr | protein | 235 | 47% helix, 17% strand | Q12GY8 |
| D | Short-chain DEHYDROGENASE/REDUCTASE sdr | protein | 248 | 51% helix, 16% strand | Q12GY8 |
Ligands and binding sites
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 4 copies · chains C, A, B, D
- FMT · Formic acid · additive · 9 copies · chains C, D, A, B
- GOL · Glycerol · additive · chains A
- PEG · Di(hydroxyethyl)ether · additive · chains B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1080 | 0.81 | 0.82 | 70 | FMT |
| 2 | 314 | 0.77 | 0.89 | 45 | NAP, PEG |
| 3 | 413 | 0.76 | 0.85 | 58 | NAP, FMT |
| 4 | 390 | 0.75 | 0.85 | 54 | FMT, NAP |
| 5 | 270 | 0.59 | 0.79 | 40 | NAP |
Interfaces
4 interfaces between chains.
- C–A · 1804 Ų buried · 23 hydrogen bonds · protein-protein
- B–D · 1784 Ų buried · 24 hydrogen bonds · protein-protein
- C–D · 1298 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 1287 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 modified (engineered).
Compared structures
- 4IQG · Crystal structure of BPRO0239 oxidoreductase from Polaromonas sp. JS666 in NADP bound form · the same entry in another collection · chain C against C, 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 Q12GY8
- Elsewhere: RCSB PDB 4IQG · PDBe 4IQG · UniProt Q12GY8
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