MolNFT v1 · #106216 · protein
Crystal structure of carbohydrate transporter MSMEG_3599 from mycobacterium smegmatis str. MC2 155, target efi-510970, in complex with D-threitol
4RSM · Periplasmic binding PROTEIN/LACI transcriptional regulator: “Crystal structure of carbohydrate transporter MSMEG_3599 from mycobacterium smegmatis str. MC2 155, target…”. X-ray diffraction, 1 ligand (3VB), 11 pockets (best…
- PDB
- 4RSM
- Type
- protein
- Length
- 1,257 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Periplasmic binding PROTEIN/LACI transcriptional regulator
- UniProt
- A0QYB5
- Ligands
- 3VB
- Pockets
- 11 · best druggability 0.82
Structure
x-ray diffraction · 3 distinct chains · 49% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Periplasmic binding PROTEIN/LACI transcriptional regulator | protein | 315 | 49% helix, 18% strand | A0QYB5 |
| C | Periplasmic binding PROTEIN/LACI transcriptional regulator | protein | 314 | 49% helix, 18% strand | A0QYB5 |
| D | Periplasmic binding PROTEIN/LACI transcriptional regulator | protein | 313 | 48% helix, 18% strand | A0QYB5 |
Ligands and binding sites
- 3VB · D-Threitol · ligand · 4 copies · chains A, B, C, D
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 | 1159 | 0.82 | 0.83 | 101 | empty |
| 2 | 1082 | 0.71 | 0.75 | 85 | empty |
| 3 | 199 | 0.51 | 0.77 | 37 | empty |
| 4 | 200 | 0.48 | 0.75 | 30 | empty |
| 5 | 144 | 0.41 | 0.75 | 25 | empty |
Interfaces
4 interfaces between chains.
- A–D · 1100 Ų buried · 18 hydrogen bonds · protein-protein
- A–C · 774 Ų buried · 14 hydrogen bonds · protein-protein
- B–D · 702 Ų buried · 17 hydrogen bonds · protein-protein
- B–C · 126 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 4RSM · Crystal structure of carbohydrate transporter msmeg_3599 from mycobacterium smegmatis… · the same entry in another collection · chain A against A, TM-score 1.00
- A0QYB5 · AlphaFold monomer V2.0 prediction for D-threitol-binding protein (A0QYB5) · a predicted model of the same protein · chain D 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 A0QYB5
- Elsewhere: RCSB PDB 4RSM · PDBe 4RSM · UniProt A0QYB5
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