MolNFT v1 · #104603 · protein
Crystal structure of dipeptide binding protein from pseudoalteromonas sp. SM9913 in complex with val-thr
4QFP · ABC transporter periplasmic peptide-binding protein: “Crystal structure of dipeptide binding protein from pseudoalteromonas sp. SM9913 in complex with val-thr”. X-ray diffraction, 1 ligand (PO4), 14 pockets (best druggability 0.85).…
- PDB
- 4QFP
- Type
- protein
- Length
- 1,018 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ABC transporter periplasmic peptide-binding protein
- UniProt
- A7Y7W1
- Ligands
- PO4
- Pockets
- 14 · best druggability 0.85
Structure
x-ray diffraction · 1 distinct chain · 30% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | ABC transporter periplasmic peptide-binding protein | protein | 509 | 30% helix, 22% strand | A7Y7W1 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 737 | 0.85 | 0.88 | 95 | GOL |
| 2 | 338 | 0.78 | 0.89 | 40 | empty |
| 3 | 60 | 0.71 | 0.97 | 18 | empty |
| 4 | 51 | 0.70 | 0.99 | 28 | GOL |
| 5 | 200 | 0.70 | 0.87 | 32 | PO4 |
Interfaces
1 interface between chains.
- A–B · 1039 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 4QFP · Crystal structure of dipeptide binding protein from pseudoalteromonas sp. SM9913 in… · 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 A7Y7W1
- Elsewhere: RCSB PDB 4QFP · PDBe 4QFP · UniProt A7Y7W1
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