Research workbench
Crystal structures of a sodium-alpha-keto acid binding subunit from a trap transporter in its closed forms
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
- 2HZL
- Type
- protein
- Length
- 671 residues
- Chains
- 2
- 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
- Ligands
- PYR, NA
- Pockets
- 3 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 53% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Trap-T family SORBITOL/MANNITOL transporter, periplasmic binding protein, smom | protein | 334 | 52% helix, 15% strand | Q3J1R2 |
| B | Trap-T family SORBITOL/MANNITOL transporter, periplasmic binding protein, smom | protein | 337 | 53% helix, 15% strand | Q3J1R2 |
Ligands and binding sites
- PYR · Pyruvic acid · ligand · 3 copies · chains A, B
- NA · Sodium ion · metal · 2 copies · chains A, 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 119 | 0.79 | 0.98 | 29 | empty |
| 2 | 180 | 0.48 | 0.76 | 19 | empty |
| 3 | 174 | 0.46 | 0.75 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 3728 Ų buried · 38 hydrogen bonds · protein-protein
Compared structures
- 2HZL · Crystal structures of a sodium-alpha-keto acid binding subunit from a TRAP transporter in… · the same entry in another collection · chain A against A, 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 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 Q3J1R2
- Elsewhere: RCSB PDB 2HZL · PDBe 2HZL · UniProt Q3J1R2
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