MolNFT v1 · #119761 · protein
S.PNEUMONIAE ABC-transporter substrate binding protein fusa apo structure
5G5Y · ABC transporter, substrate-binding protein: “S.PNEUMONIAE ABC-transporter substrate binding protein fusa apo structure”. X-ray diffraction, 3 ligands (ZN, CA, SO4), 11 pockets (best druggability 0.62). MolNFT v1 #119761 on…
- PDB
- 5G5Y
- Type
- protein
- Length
- 988 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ABC transporter, substrate-binding protein
- UniProt
- A0A0H2URD6
- Ligands
- ZN, CA, SO4
- Pockets
- 11 · best druggability 0.62
Structure
x-ray diffraction · 1 distinct chain · 45% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | ABC transporter, substrate-binding protein | protein | 494 | 45% helix, 14% strand | A0A0H2URD6 |
Ligands and binding sites
- ZN · Zinc ion · metal · 10 copies · chains A, B
- CA · Calcium ion · metal · 4 copies · chains A, B
- SO4 · Sulfate ion · ion · chains A, B
- GOL · Glycerol · additive · 5 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 168 | 0.62 | 0.84 | 30 | empty |
| 2 | 181 | 0.61 | 0.83 | 30 | GOL |
| 3 | 239 | 0.54 | 0.77 | 31 | empty |
| 4 | 138 | 0.49 | 0.79 | 23 | SO4 |
| 5 | 201 | 0.48 | 0.75 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 439 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 5G5Y · S.pneumoniae ABC-transporter substrate binding protein FusA apo structure · 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
- Every structure of UniProt A0A0H2URD6
- Elsewhere: RCSB PDB 5G5Y · PDBe 5G5Y · UniProt A0A0H2URD6
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