MolNFT v1 · #102020 · protein
Crystal structure of a trap periplasmic solute binding protein from rhodopseudomonas palustris HAA2 (RPB_3329), target efi-510223, with bound succinate
4O94 · Trap dicarboxylate transporter dctp subunit: “Crystal structure of a trap periplasmic solute binding protein from rhodopseudomonas palustris HAA2…”. X-ray diffraction, 1 ligand (CL), 10 pockets (best druggability 0.65). MolNFT v1…
- PDB
- 4O94
- Type
- protein
- Length
- 1,223 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Trap dicarboxylate transporter dctp subunit
- UniProt
- Q2IUT5
- Ligands
- CL
- Pockets
- 10 · best druggability 0.65
Structure
x-ray diffraction · 3 distinct chains · 50% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Trap dicarboxylate transporter dctp subunit | protein | 309 | 50% helix, 19% strand | Q2IUT5 |
| B | Trap dicarboxylate transporter dctp subunit | protein | 304 | 50% helix, 19% strand | Q2IUT5 |
| C, D | Trap dicarboxylate transporter dctp subunit | protein | 305 | 50% helix, 19% strand | Q2IUT5 |
Ligands and binding sites
- CL · Chloride ion · ion · 15 copies · chains A, B, C, D
- SIN · Succinic acid · additive · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 460 | 0.65 | 0.77 | 51 | CL |
| 2 | 443 | 0.60 | 0.75 | 49 | empty |
| 3 | 323 | 0.59 | 0.77 | 34 | CL |
| 4 | 164 | 0.44 | 0.75 | 27 | empty |
| 5 | 90 | 0.39 | 0.77 | 21 | empty |
Interfaces
3 interfaces between chains.
- B–D · 595 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 508 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 342 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 28 modified (engineered).
Compared structures
- 4O94 · 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 Q2IUT5
- Elsewhere: RCSB PDB 4O94 · PDBe 4O94 · UniProt Q2IUT5
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