MolNFT v1 · #102061 · protein
Crystal structure of a trap periplasmic solute binding protein from rhodopseudomonas palustris HAA2 (RPB_2686), target efi-510221, with density modeled as (S)-2-hydroxy-2-methyl-3-oxobutanoate ((S)-2- acetolactate)
4OAN · Trap dicarboxylate transporter dctp subunit: “Crystal structure of a trap periplasmic solute binding protein from rhodopseudomonas palustris HAA2…”. X-ray diffraction, 2 ligands (X2X, CL), 4 pockets (best druggability 0.72). MolNFT…
- PDB
- 4OAN
- Type
- protein
- Length
- 622 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Trap dicarboxylate transporter dctp subunit
- UniProt
- Q2IWM2
- Ligands
- X2X, CL
- Pockets
- 4 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 50% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Trap dicarboxylate transporter dctp subunit | protein | 312 | 50% helix, 16% strand | Q2IWM2 |
| B | Trap dicarboxylate transporter dctp subunit | protein | 310 | 51% helix, 17% strand | Q2IWM2 |
Ligands and binding sites
- X2X · (2S)-2-hydroxy-2-methyl-3-oxobutanoic acid · ligand · 2 copies · chains A, B
- CL · Chloride ion · ion · chains A
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 53 | 0.72 | 0.99 | 21 | X2X |
| 2 | 512 | 0.70 | 0.80 | 50 | empty |
| 3 | 66 | 0.31 | 0.74 | 13 | empty |
| 4 | 56 | 0.30 | 0.75 | 12 | empty |
Interfaces
1 interface between chains.
- A–B · 278 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 15 modified (engineered).
Compared structures
- 4OAN · Crystal structure of a TRAP periplasmic solute binding protein from rhodopseudomonas… · 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 Q2IWM2
- Elsewhere: RCSB PDB 4OAN · PDBe 4OAN · UniProt Q2IWM2
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