MolNFT v1 · #101969 · protein
Crystal structure of a trap periplasmic solute binding protein from shewanella loihica pv-4, target efi-510273, with bound L-malate
4O7M · Trap dicarboxylate transporter, dctp subunit: “Crystal structure of a trap periplasmic solute binding protein from shewanella loihica pv-4, target…”. X-ray diffraction, 2 ligands (LMR, SO4), 10 pockets (best druggability 0.72).…
- PDB
- 4O7M
- Type
- protein
- Length
- 1,195 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Trap dicarboxylate transporter, dctp subunit
- UniProt
- A3QCW5
- Ligands
- LMR, SO4
- Pockets
- 10 · best druggability 0.72
Structure
x-ray diffraction · 4 distinct chains · 50% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Trap dicarboxylate transporter, dctp subunit | protein | 304 | 50% helix, 21% strand | A3QCW5 |
| B | Trap dicarboxylate transporter, dctp subunit | protein | 305 | 50% helix, 19% strand | A3QCW5 |
| C | Trap dicarboxylate transporter, dctp subunit | protein | 283 | 47% helix, 23% strand | A3QCW5 |
| D | Trap dicarboxylate transporter, dctp subunit | protein | 303 | 50% helix, 19% strand | A3QCW5 |
Ligands and binding sites
- LMR · (2S)-2-hydroxybutanedioic acid · ligand · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · chains B
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 | 599 | 0.72 | 0.80 | 66 | empty |
| 2 | 536 | 0.64 | 0.76 | 53 | empty |
| 3 | 138 | 0.50 | 0.79 | 27 | empty |
| 4 | 93 | 0.46 | 0.80 | 22 | empty |
| 5 | 89 | 0.42 | 0.78 | 20 | empty |
Interfaces
6 interfaces between chains.
- B–C · 520 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 484 Ų buried · 10 hydrogen bonds · protein-protein
- B–D · 443 Ų buried · 5 hydrogen bonds · protein-protein
- A–D · 392 Ų buried · 3 hydrogen bonds · protein-protein
- A–B · 373 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 28 modified (engineered).
Compared structures
- 4O7M · 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 4O7M · PDBe 4O7M · UniProt A3QCW5
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