Research workbench
Flavoredoxin of desulfovibrio vulgaris (miyazaki F)
Analyse Flavoredoxin of desulfovibrio vulgaris (miyazaki F) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2D5M
- Type
- protein
- Length
- 183 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Flavoredoxin
- Ligands
- FMN, ZN
- Pockets
- 2 · best druggability 0.46
Structure
x-ray diffraction · 1 distinct chain · 17% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Flavoredoxin | protein | 183 | 17% helix, 39% strand | — |
Ligands and binding sites
- FMN · Flavin mononucleotide · ligand · chains A
- ZN · Zinc ion · metal · 3 copies · chains A
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 163 | 0.46 | 0.76 | 28 | FMN, MES |
| 2 | 125 | 0.41 | 0.74 | 20 | empty |
Compared structures
- 2D5M · Flavoredoxin of Desulfovibrio vulgaris (Miyazaki F) · 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 2D5M · PDBe 2D5M
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