MolNFT v1 · #119763 · protein
S.PNEUMONIAE ABC-transporter substrate binding protein fusa in complex with nystose
5G60 · ABC transporter, substrate-binding protein: “S.PNEUMONIAE ABC-transporter substrate binding protein fusa in complex with nystose”. X-ray diffraction, 4 ligands (FRU, GLC, CA), 20 pockets (best druggability 0.76). MolNFT v1 #119763…
- PDB
- 5G60
- Type
- protein
- Length
- 1,955 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, CL
- Pockets
- 20 · best druggability 0.76
Structure
x-ray diffraction · 4 distinct chains · 45% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ABC transporter, substrate-binding protein | protein | 488 | 45% helix, 14% strand | A0A0H2URD6 |
| B | ABC transporter, substrate-binding protein | protein | 489 | 45% helix, 14% strand | A0A0H2URD6 |
| C | ABC transporter, substrate-binding protein | protein | 491 | 45% helix, 14% strand | A0A0H2URD6 |
| D | ABC transporter, substrate-binding protein | protein | 487 | 45% helix, 14% strand | A0A0H2URD6 |
Ligands and binding sites
- FRU · beta-D-fructofuranose · sugar · 12 copies · chains A, B, C, D
- GLC · alpha-D-glucopyranose · sugar · 4 copies · chains A, B, C, D
- CA · Calcium ion · metal · 8 copies · chains A, B, C, D
- CL · Chloride ion · ion · chains A, B
- GOL · Glycerol · additive · 4 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, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 927 | 0.76 | 0.79 | 82 | GLC, FRU |
| 2 | 1134 | 0.74 | 0.77 | 90 | GLC, FRU, GOL |
| 3 | 398 | 0.69 | 0.81 | 46 | FRU |
| 4 | 362 | 0.69 | 0.82 | 46 | GLC, FRU |
| 5 | 510 | 0.67 | 0.78 | 52 | empty |
Interfaces
5 interfaces between chains.
- A–B · 728 Ų buried · 10 hydrogen bonds · protein-protein
- C–D · 683 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 218 Ų buried · 3 hydrogen bonds · protein-protein
- B–D · 148 Ų buried · 1 hydrogen bond · protein-protein
- A–D · 133 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 5G60 · S.pneumoniae ABC-transporter substrate binding protein FusA in complex with nystose · 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 5G60 · PDBe 5G60 · UniProt A0A0H2URD6
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.