Research workbench
Crystal structures of a sodium-alpha-keto acid binding subunit from a trap transporter in its open form
Analyse Crystal structures of a sodium-alpha-keto acid binding subunit from a trap… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2HZK
- Type
- protein
- Length
- 1,343 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Trap-T family SORBITOL/MANNITOL transporter, periplasmic binding protein, smom
- UniProt
- Q3J1R2
- Pockets
- 12 · best druggability 0.82
Structure
x-ray diffraction · 4 distinct chains · 54% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Trap-T family SORBITOL/MANNITOL transporter, periplasmic binding protein, smom | protein | 334 | 54% helix, 15% strand | Q3J1R2 |
| B | Trap-T family SORBITOL/MANNITOL transporter, periplasmic binding protein, smom | protein | 336 | 54% helix, 16% strand | Q3J1R2 |
| C | Trap-T family SORBITOL/MANNITOL transporter, periplasmic binding protein, smom | protein | 335 | 55% helix, 16% strand | Q3J1R2 |
| D | Trap-T family SORBITOL/MANNITOL transporter, periplasmic binding protein, smom | protein | 338 | 54% helix, 15% strand | Q3J1R2 |
Ligands and binding sites
- GOL · Glycerol · additive · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 165 | 0.82 | 0.97 | 27 | empty |
| 2 | 164 | 0.81 | 0.97 | 26 | empty |
| 3 | 543 | 0.75 | 0.82 | 50 | GOL |
| 4 | 339 | 0.66 | 0.80 | 38 | GOL |
| 5 | 287 | 0.64 | 0.80 | 36 | GOL |
Interfaces
3 interfaces between chains.
- C–D · 3812 Ų buried · 46 hydrogen bonds · protein-protein
- A–B · 3781 Ų buried · 46 hydrogen bonds · protein-protein
- A–D · 815 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 40 modified (engineered).
Compared structures
- 2HZK · Crystal structures of a sodium-alpha-keto acid binding subunit from a TRAP transporter in… · the same entry in another collection · chain D against D, TM-score 1.00
- Q3J1R2 · AlphaFold monomer V2.0 prediction for alpha-keto acid-binding periplasmic protein takp… · a predicted model of the same protein · chain D against A, TM-score 0.96
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 Q3J1R2
- Elsewhere: RCSB PDB 2HZK · PDBe 2HZK · UniProt Q3J1R2
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.