Research workbench
Crystal structure of a trap periplasmic solute binding protein from shewanella loihica pv-4 (SHEW_1446), target efi-510273, with bound succinate
Analyse Crystal structure of a trap periplasmic solute binding protein from shewanella… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4OA4
- Type
- protein
- Length
- 1,217 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Trap dicarboxylate transporter, dctp subunit
- UniProt
- A3QCW5
- Ligands
- CL
- Pockets
- 10 · best druggability 0.76
Structure
x-ray diffraction · 3 distinct chains · 50% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Trap dicarboxylate transporter, dctp subunit | protein | 304 | 50% helix, 19% strand | A3QCW5 |
| B, C | Trap dicarboxylate transporter, dctp subunit | protein | 305 | 50% helix, 19% strand | A3QCW5 |
| D | Trap dicarboxylate transporter, dctp subunit | protein | 303 | 50% helix, 21% strand | A3QCW5 |
Ligands and binding sites
- CL · Chloride ion · ion · 9 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1086 | 0.76 | 0.78 | 99 | CL |
| 2 | 587 | 0.66 | 0.76 | 48 | empty |
| 3 | 99 | 0.45 | 0.79 | 18 | empty |
| 4 | 93 | 0.43 | 0.79 | 19 | empty |
| 5 | 80 | 0.40 | 0.78 | 17 | empty |
Interfaces
6 interfaces between chains.
- A–C · 511 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 507 Ų buried · 3 hydrogen bonds · protein-protein
- A–D · 457 Ų buried · 4 hydrogen bonds · protein-protein
- B–D · 457 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 353 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 28 modified (engineered).
Compared structures
- 4OA4 · CRYSTAL STRUCTURE OF A TRAP PERIPLASMIC SOLUTE BINDING PROTEIN FROM SHEWANELLA LOIHICA… · the same entry in another collection · chain D against D, TM-score 1.00
- A3QCW5 · AlphaFold monomer V2.0 prediction for C4-dicarboxylate-binding periplasmic protein dctp… · a predicted model of the same protein · chain B 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 A3QCW5
- Elsewhere: RCSB PDB 4OA4 · PDBe 4OA4 · UniProt A3QCW5
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