Research workbench
Staphyloferrin B precursor biosynthetic enzyme sbna bound to plp
Analyse Staphyloferrin B precursor biosynthetic enzyme sbna bound to plp in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5D84
- Type
- protein
- Length
- 318 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Probable siderophore biosynthesis protein sbna
- UniProt
- A6QDA0
- Ligands
- PLP, MG
- Pockets
- 2 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 42% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Probable siderophore biosynthesis protein sbna | protein | 318 | 42% helix, 16% strand | A6QDA0 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 708 | 0.78 | 0.82 | 64 | PLP |
| 2 | 58 | 0.29 | 0.74 | 12 | empty |
Modifications
Observed in the structure: 1 cofactor (pyridoxal phosphate Schiff base).
Compared structures
- 5D84 · Staphyloferrin B precursor biosynthetic enzyme SbnA bound to PLP · the same entry in another collection · chain A against A, TM-score 1.00
- A6QDA0 · AlphaFold monomer V2.0 prediction for N-(2-amino-2-carboxyethyl)-L-glutamate synthase… · a predicted model of the same protein · 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 A6QDA0
- Elsewhere: RCSB PDB 5D84 · PDBe 5D84 · UniProt A6QDA0
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