MolNFT v1 · #103384 · protein
Crystal structure of a trap periplasmic solute binding protein from roseobacter denitrificans (RD1_0742, target efi-510239) with bound 3- deoxy-D-manno-oct-2-ulosonic acid (kdo)
4PF6 · C4-dicarboxylate-binding protein: “Crystal structure of a trap periplasmic solute binding protein from roseobacter denitrificans (RD1_0742…”. X-ray diffraction, 2 ligands (KDO, SO4), 2 pockets (best druggability 0.68). MolNFT v1…
- PDB
- 4PF6
- Type
- protein
- Length
- 305 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- C4-dicarboxylate-binding protein
- UniProt
- Q16C67
- Ligands
- KDO, SO4
- Pockets
- 2 · best druggability 0.68
Structure
x-ray diffraction · 1 distinct chain · 50% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | C4-dicarboxylate-binding protein | protein | 305 | 50% helix, 20% strand | Q16C67 |
Ligands and binding sites
- KDO · 3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid · sugar · chains A
- SO4 · Sulfate ion · ion · 2 copies · chains A
- PGE · Triethylene glycol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 139 | 0.68 | 0.89 | 31 | KDO |
| 2 | 68 | 0.32 | 0.74 | 16 | PGE |
Modifications
Observed in the structure: 7 modified (engineered).
Compared structures
- 4PF6 · Crystal structure of a trap periplasmic solute binding protein from roseobacter… · 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 Q16C67
- Elsewhere: RCSB PDB 4PF6 · PDBe 4PF6 · UniProt Q16C67
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