MolNFT v1 · #104598 · protein
Crystal structure of dipeptide binding protein from pseudoalteromonas sp. SM9913
4QFK · ABC transporter periplasmic peptide-binding protein: “Crystal structure of dipeptide binding protein from pseudoalteromonas sp. SM9913”. X-ray diffraction, 20 pockets (best druggability 0.81). MolNFT v1 #104598 on GenesisL1: 3D…
- PDB
- 4QFK
- Type
- protein
- Length
- 4,040 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ABC transporter periplasmic peptide-binding protein
- UniProt
- A7Y7W1
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 31% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H, A, B, C, D, E, F, G | ABC transporter periplasmic peptide-binding protein | protein | 505 | 31% helix, 21% strand | A7Y7W1 |
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 582 | 0.81 | 0.86 | 85 | empty |
| 2 | 961 | 0.81 | 0.82 | 103 | empty |
| 3 | 918 | 0.77 | 0.80 | 83 | empty |
| 4 | 335 | 0.76 | 0.87 | 46 | empty |
| 5 | 918 | 0.75 | 0.79 | 86 | empty |
Interfaces
13 interfaces between chains.
- A–C · 873 Ų buried · 15 hydrogen bonds · protein-protein
- H–D · 861 Ų buried · 12 hydrogen bonds · protein-protein
- H–C · 696 Ų buried · 7 hydrogen bonds · protein-protein
- H–A · 664 Ų buried · 9 hydrogen bonds · protein-protein
- C–D · 655 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide (disulfide).
Compared structures
- 4QFK · Crystal structure of dipeptide binding protein from pseudoalteromonas sp. SM9913 · the same entry in another collection · chain H against H, 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 4QFK · PDBe 4QFK · UniProt A7Y7W1
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