Research workbench
SYRB2 with FE(II), bromide, and alpha-ketoglutarate
Analyse SYRB2 with FE(II), bromide, and alpha-ketoglutarate in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2FCV
- Type
- protein
- Length
- 603 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Syringomycin biosynthesis enzyme 2
- Ligands
- AKG, DSU, FE2, BR
- Pockets
- 10 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 18% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Syringomycin biosynthesis enzyme 2 | protein | 304 | 18% helix, 28% strand | — |
| B | Syringomycin biosynthesis enzyme 2 | protein | 299 | 18% helix, 29% strand | — |
Ligands and binding sites
- AKG · 2-oxoglutaric acid · ligand · 2 copies · chains A, B
- DSU · ((2R,3S,4S,5S)-3,4-dihydroxy-5-(hydroxymethyl)-5-((2R,3S,4S,5S,6R)-3,4,5-trihydroxy-6-methoxy-tetrahydro-2H-pyran-2-yloxy)-tetrahydrofuran-2-yl)methyl nonanoate · ligand · chains A
- FE2 · Fe (II) ion · metal · 2 copies · chains A, B
- BR · Bromide ion · ion · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 82 | 0.75 | 0.98 | 28 | FE2, BR, AKG |
| 2 | 71 | 0.75 | 0.99 | 28 | BR, AKG |
| 3 | 636 | 0.70 | 0.78 | 80 | empty |
| 4 | 328 | 0.63 | 0.80 | 39 | empty |
| 5 | 188 | 0.46 | 0.75 | 30 | empty |
Interfaces
1 interface between chains.
- A–B · 873 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 2FCV · SyrB2 with Fe(II), bromide, and alpha-ketoglutarate · the same entry in another collection · chain B against B, 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 2FCV · PDBe 2FCV
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