Research workbench
Crystal structure of glycine betaine, L-proline ABC transporter, GLYCINE/BETAINE/L-proline-binding protein (prox) from borrelia burgdorferi
Analyse Crystal structure of glycine betaine, L-proline ABC transporter… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3TMG
- Type
- protein
- Length
- 1,061 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycine betaine, L-proline ABC transporter, GLYCINE/BETAINE/L-proline-binding protein…
- UniProt
- O51169
- Ligands
- BET, UNL
- Pockets
- 8 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 46% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glycine betaine, L-proline ABC transporter, GLYCINE/BETAINE/L-proline-binding protein (prox) | protein | 266 | 45% helix, 24% strand | O51169 |
| B, C, D | Glycine betaine, L-proline ABC transporter, GLYCINE/BETAINE/L-proline-binding protein (prox) | protein | 265 | 46% helix, 23% strand | O51169 |
Ligands and binding sites
- BET · Trimethyl glycine · ligand · 4 copies · chains A, B, C, D
- UNL · Unknown ligand · ion · chains D
- EDO · 1,2-ethanediol · additive · 2 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1172 | 0.79 | 0.80 | 102 | EDO |
| 2 | 98 | 0.77 | 0.97 | 27 | BET, UNL |
| 3 | 1121 | 0.76 | 0.78 | 106 | empty |
| 4 | 825 | 0.73 | 0.78 | 76 | empty |
| 5 | 56 | 0.72 | 0.98 | 14 | BET |
Interfaces
3 interfaces between chains.
- C–D · 514 Ų buried · 11 hydrogen bonds · protein-protein
- B–D · 487 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 484 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 3TMG · Crystal structure of Glycine betaine, L-proline ABC transporter… · 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 O51169
- Elsewhere: RCSB PDB 3TMG · PDBe 3TMG · UniProt O51169
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