MolNFT v1 · #106408 · protein
Crystal structure of 5-methylthioribose transporter solute binding protein TLET_1677 from thermotoga lettingae tmo target efi-511109 in complex with 5-methylthioribose
4RY8 · Periplasmic binding protein: “Crystal structure of 5-methylthioribose transporter solute binding protein TLET_1677 from thermotoga…”. X-ray diffraction, 1 ligand (SR1), 10 pockets (best druggability 0.77). MolNFT v1 #106408 on…
- PDB
- 4RY8
- Type
- protein
- Length
- 1,276 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Periplasmic binding protein
- UniProt
- A8F7U7
- Ligands
- SR1
- Pockets
- 10 · best druggability 0.77
Structure
x-ray diffraction · 3 distinct chains · 49% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Periplasmic binding protein | protein | 315 | 50% helix, 20% strand | A8F7U7 |
| B, D | Periplasmic binding protein | protein | 321 | 50% helix, 19% strand | A8F7U7 |
| C | Periplasmic binding protein | protein | 319 | 48% helix, 19% strand | A8F7U7 |
Ligands and binding sites
- SR1 · 5-S-methyl-5-thio-alpha-D-ribofuranose · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 567 | 0.77 | 0.84 | 56 | empty |
| 2 | 380 | 0.76 | 0.86 | 54 | empty |
| 3 | 487 | 0.75 | 0.83 | 58 | empty |
| 4 | 52 | 0.73 | 0.99 | 15 | SR1 |
| 5 | 283 | 0.72 | 0.86 | 44 | empty |
Interfaces
6 interfaces between chains.
- A–C · 1126 Ų buried · 11 hydrogen bonds · protein-protein
- B–D · 1114 Ų buried · 10 hydrogen bonds · protein-protein
- A–D · 456 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 422 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 35 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4RY8 · Crystal structure of 5-methylthioribose transporter solute binding protein TLET_1677 from… · 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 A8F7U7
- Elsewhere: RCSB PDB 4RY8 · PDBe 4RY8 · UniProt A8F7U7
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