MolNFT v1 · #119764 · protein
S.PNEUMONIAE ABC-transporter substrate binding protein fusa in complex with fructo-nystose
5G61 · ABC transporter, substrate-binding protein: “S.PNEUMONIAE ABC-transporter substrate binding protein fusa in complex with fructo-nystose”. X-ray diffraction, 4 ligands (ZEE, UEA, FRU), 20 pockets (best druggability 0.76). MolNFT v1…
- PDB
- 5G61
- Type
- protein
- Length
- 1,960 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ABC transporter, substrate-binding protein
- UniProt
- A0A0H2URD6
- Ligands
- ZEE, UEA, FRU, CA
- Pockets
- 20 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 45% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | ABC transporter, substrate-binding protein | protein | 490 | 45% helix, 14% strand | A0A0H2URD6 |
Ligands and binding sites
- ZEE · beta-L-talopyranose · ligand · 4 copies · chains A, B, C, D
- UEA · beta-D-sorbofuranose · ligand · 4 copies · chains B, C
- FRU · beta-D-fructofuranose · sugar · 12 copies · chains A, B, C, D
- CA · Calcium ion · metal · 8 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, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1066 | 0.76 | 0.79 | 101 | ZEE, UEA, FRU |
| 2 | 510 | 0.74 | 0.82 | 60 | empty |
| 3 | 672 | 0.74 | 0.80 | 67 | empty |
| 4 | 1153 | 0.73 | 0.76 | 105 | empty |
| 5 | 333 | 0.70 | 0.83 | 49 | UEA, FRU |
Interfaces
5 interfaces between chains.
- B–D · 1504 Ų buried · 22 hydrogen bonds · protein-protein
- A–C · 1473 Ų buried · 23 hydrogen bonds · protein-protein
- A–D · 109 Ų buried · 0 hydrogen bonds · protein-protein
- B–C · 104 Ų buried · 0 hydrogen bonds · protein-protein
- A–B · 89 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 5G61 · S.pneumoniae ABC-transporter substrate binding protein FusA in complex with fructo-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 5G61 · PDBe 5G61 · UniProt A0A0H2URD6
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