Research workbench
Crystal structure of FMN-bound dszc from rhodococcus erythropolis D-1
Analyse Crystal structure of FMN-bound dszc from rhodococcus erythropolis D-1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3X0Y
- Type
- protein
- Length
- 3,206 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dszc
- Ligands
- FMN
- Pockets
- 20 · best druggability 0.88
Structure
x-ray diffraction · 3 distinct chains · 57% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Dszc | protein | 402 | 57% helix, 10% strand | — |
| B, C, F, H | Dszc | protein | 400 | 57% helix, 11% strand | — |
| E, G | Dszc | protein | 401 | 58% helix, 10% strand | — |
Ligands and binding sites
- FMN · Flavin mononucleotide · ligand · 4 copies · chains A, F, C, E, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1083 | 0.88 | 0.90 | 146 | FMN |
| 2 | 477 | 0.86 | 0.92 | 82 | empty |
| 3 | 467 | 0.85 | 0.92 | 72 | FMN |
| 4 | 483 | 0.85 | 0.92 | 69 | FMN |
| 5 | 560 | 0.84 | 0.90 | 84 | empty |
Interfaces
21 interfaces between chains.
- A–F · 2142 Ų buried · 16 hydrogen bonds · protein-protein
- B–D · 2109 Ų buried · 17 hydrogen bonds · protein-protein
- C–E · 2084 Ų buried · 14 hydrogen bonds · protein-protein
- G–H · 2052 Ų buried · 16 hydrogen bonds · protein-protein
- D–E · 1524 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 3X0Y · Crystal structure of FMN-bound DszC from Rhodococcus erythropolis D-1 · 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
- Elsewhere: RCSB PDB 3X0Y · PDBe 3X0Y
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