MolNFT v1 · #118434 · protein
Crystal structure of periplasmic dipeptide transport protein from yersinia pestis
5F1Q: “Crystal structure of periplasmic dipeptide transport protein from yersinia pestis”. X-ray diffraction, 1 ligand (CL), 9 pockets (best druggability 0.73). MolNFT v1 #118434 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 5F1Q
- Type
- protein
- Length
- 1,024 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Periplasmic dipeptide transport protein
- UniProt
- A0A0H2YM47
- Ligands
- CL
- Pockets
- 9 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 33% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Periplasmic dipeptide transport protein | protein | 515 | 32% helix, 23% strand | A0A0H2YM47 |
| B | Periplasmic dipeptide transport protein | protein | 509 | 33% helix, 22% strand | A0A0H2YM47 |
Ligands and binding sites
- CL · Chloride ion · ion · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 13 copies · chains A, B
- GOL · Glycerol · additive · chains A
- PEG · Di(hydroxyethyl)ether · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 82 | 0.73 | 0.96 | 27 | empty |
| 2 | 83 | 0.72 | 0.96 | 28 | empty |
| 3 | 249 | 0.64 | 0.82 | 34 | empty |
| 4 | 240 | 0.62 | 0.81 | 37 | empty |
| 5 | 133 | 0.44 | 0.76 | 25 | EDO |
Interfaces
1 interface between chains.
- A–B · 797 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 32 modified, 4 disulfide (engineered, disulfide).
Compared structures
- 5F1Q · Crystal Structure of Periplasmic Dipeptide Transport Protein from Yersinia pestis · 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 A0A0H2YM47
- Elsewhere: RCSB PDB 5F1Q · PDBe 5F1Q · UniProt A0A0H2YM47
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