MolNFT v1 · #115516 · protein
Crystal structure of a trap periplasmic solute binding protein from pseudoalteromonas atlantica T6C(PATL_2292, target efi-510180) with bound sodium and pyruvate
5CM6 · Trap dicarboxylate transporter-dctp subunit: “Crystal structure of a trap periplasmic solute binding protein from pseudoalteromonas atlantica…”. X-ray diffraction, 2 ligands (PYR, NA), 6 pockets (best druggability 0.75). MolNFT v1…
- PDB
- 5CM6
- Type
- protein
- Length
- 660 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Trap dicarboxylate transporter-dctp subunit
- UniProt
- Q15TH9
- Ligands
- PYR, NA
- Pockets
- 6 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 55% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Trap dicarboxylate transporter-dctp subunit | protein | 331 | 54% helix, 15% strand | Q15TH9 |
| B | Trap dicarboxylate transporter-dctp subunit | protein | 329 | 56% helix, 15% strand | Q15TH9 |
Ligands and binding sites
- PYR · Pyruvic acid · ligand · 2 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
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 81 | 0.75 | 0.98 | 28 | empty |
| 2 | 269 | 0.60 | 0.79 | 39 | empty |
| 3 | 106 | 0.53 | 0.83 | 24 | empty |
| 4 | 171 | 0.51 | 0.78 | 26 | empty |
| 5 | 175 | 0.48 | 0.76 | 25 | empty |
Interfaces
1 interface between chains.
- A–B · 2955 Ų buried · 24 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 30 modified (engineered).
Compared structures
- 5CM6 · CRYSTAL STRUCTURE OF A TRAP PERIPLASMIC SOLUTE BINDING PROTEIN FROM PSEUDOALTEROMONAS… · 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 Q15TH9
- Elsewhere: RCSB PDB 5CM6 · PDBe 5CM6 · UniProt Q15TH9
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