MolNFT v1 · #116260 · protein
Staphyloferrin B precursor biosynthetic enzyme sbna Y152F/S185G variant
5D87 · Probable siderophore biosynthesis protein sbna: “Staphyloferrin B precursor biosynthetic enzyme sbna Y152F/S185G variant”. X-ray diffraction, 3 ligands (PLP, MG, K), 2 pockets (best druggability 0.76). MolNFT v1 #116260 on…
- PDB
- 5D87
- Type
- protein
- Length
- 316 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, K
- Pockets
- 2 · best druggability 0.76
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 | 316 | 42% helix, 16% strand | A6QDA0 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · chains A
- MG · Magnesium ion · metal · 3 copies · chains A
- K · Potassium ion · metal · 2 copies · 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 481 | 0.76 | 0.84 | 62 | PLP, K |
| 2 | 63 | 0.31 | 0.75 | 13 | MG |
Modifications
Observed in the structure: 1 cofactor (pyridoxal phosphate Schiff base).
Compared structures
- 5D87 · Staphyloferrin B precursor biosynthetic enzyme SbnA Y152F/S185G variant · 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 0.99
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 5D87 · PDBe 5D87 · UniProt A6QDA0
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