MolNFT v1 · #119762 · protein
S.PNEUMONIAE ABC-transporter substrate binding protein fusa in complex with kestose
5G5Z · ABC transporter, substrate-binding protein: “S.PNEUMONIAE ABC-transporter substrate binding protein fusa in complex with kestose”. X-ray diffraction, 3 ligands (FRU, GLC, CA), 20 pockets (best druggability 0.83). MolNFT v1 #119762…
- PDB
- 5G5Z
- Type
- protein
- Length
- 1,964 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ABC transporter, substrate-binding protein
- UniProt
- A0A0H2URD6
- Ligands
- FRU, GLC, CA
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 1 distinct chain · 46% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | ABC transporter, substrate-binding protein | protein | 491 | 46% helix, 14% strand | A0A0H2URD6 |
Ligands and binding sites
- FRU · beta-D-fructofuranose · sugar · 8 copies · chains A, B, C, D
- GLC · alpha-D-glucopyranose · sugar · 4 copies · chains A, B, C, D
- CA · Calcium ion · metal · 9 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 997 | 0.83 | 0.84 | 110 | GLC, FRU |
| 2 | 930 | 0.77 | 0.80 | 96 | GLC, FRU |
| 3 | 917 | 0.77 | 0.79 | 83 | GLC, FRU |
| 4 | 431 | 0.67 | 0.79 | 58 | CA |
| 5 | 491 | 0.65 | 0.77 | 66 | empty |
Interfaces
4 interfaces between chains.
- B–C · 1511 Ų buried · 23 hydrogen bonds · protein-protein
- A–C · 662 Ų buried · 7 hydrogen bonds · protein-protein
- C–D · 570 Ų buried · 7 hydrogen bonds · protein-protein
- A–D · 233 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 5G5Z · S.pneumoniae ABC-transporter substrate binding protein FusA in complex with kestose · 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 5G5Z · PDBe 5G5Z · UniProt A0A0H2URD6
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