Research workbench
Tmox in complex with tmao
Analyse Tmox in complex with tmao in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4XZ6
- Type
- protein
- Length
- 581 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycine BETAINE/PROLINE ABC transporter, periplasmic substrate-binding protein
- UniProt
- Q5LT66
- Ligands
- TMO, CA
- Pockets
- 3 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glycine BETAINE/PROLINE ABC transporter, periplasmic substrate-binding protein | protein | 291 | 41% helix, 20% strand | Q5LT66 |
| B | Glycine BETAINE/PROLINE ABC transporter, periplasmic substrate-binding protein | protein | 290 | 39% helix, 20% strand | Q5LT66 |
Ligands and binding sites
- TMO · trimethylamine oxide · ligand · 2 copies · chains A, B
- CA · Calcium ion · metal · 2 copies · chains A, B
- GOL · Glycerol · additive · 2 copies · chains A
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 535 | 0.71 | 0.80 | 64 | empty |
| 2 | 358 | 0.63 | 0.79 | 41 | empty |
| 3 | 71 | 0.30 | 0.74 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 429 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 4XZ6 · TmoX in complex with TMAO · 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 Q5LT66
- Elsewhere: RCSB PDB 4XZ6 · PDBe 4XZ6 · UniProt Q5LT66
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