Research workbench
Crystal structure of a putative NAD(P)H:FMN oxidoreductase (SE1966) from staphylococcus epidermidis atcc 12228 at 2.00 a resolution
Analyse Crystal structure of a putative NAD(P)H:FMN oxidoreductase (SE1966) from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3GBH
- Type
- protein
- Length
- 847 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NAD(P)H-flavin oxidoreductase
- UniProt
- Q8CN78
- Ligands
- FMN, UNL, CA
- Pockets
- 5 · best druggability 0.74
Structure
x-ray diffraction · 3 distinct chains · 49% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | NAD(P)H-flavin oxidoreductase | protein | 212 | 49% helix, 17% strand | Q8CN78 |
| B | NAD(P)H-flavin oxidoreductase | protein | 213 | 48% helix, 17% strand | Q8CN78 |
| C, D | NAD(P)H-flavin oxidoreductase | protein | 211 | 49% helix, 18% strand | Q8CN78 |
Ligands and binding sites
- FMN · Flavin mononucleotide · ligand · 4 copies · chains A, B, C, D
- UNL · Unknown ligand · ligand · 4 copies · chains A, B, C, D
- CA · Calcium ion · metal · 5 copies · chains B, D
- GOL · Glycerol · additive · 6 copies · chains A, B, C, D
- PGE · Triethylene glycol · additive · 2 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 662 | 0.74 | 0.80 | 65 | UNL, GOL, FMN |
| 2 | 715 | 0.74 | 0.79 | 70 | UNL, GOL, FMN |
| 3 | 732 | 0.73 | 0.79 | 71 | FMN, UNL, GOL |
| 4 | 681 | 0.73 | 0.79 | 64 | FMN, UNL, GOL |
| 5 | 150 | 0.41 | 0.74 | 25 | empty |
Interfaces
4 interfaces between chains.
- A–B · 3300 Ų buried · 49 hydrogen bonds · protein-protein
- C–D · 3253 Ų buried · 56 hydrogen bonds · protein-protein
- A–C · 343 Ų buried · 5 hydrogen bonds · protein-protein
- A–D · 95 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 38 modified (engineered).
Compared structures
- 3GBH · Crystal structure of a putative NAD(P)H:FMN oxidoreductase (SE1966) from staphylococcus… · 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 Q8CN78
- Elsewhere: RCSB PDB 3GBH · PDBe 3GBH · UniProt Q8CN78
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