MolNFT v1 · #100179 · protein
Crystal structure of periplasmic binding protein type 1 from bordetella pertussis tohama I
4MPT · Putative LEU/ILE/VAL-binding protein: “Crystal structure of periplasmic binding protein type 1 from bordetella pertussis tohama I”. X-ray diffraction, 1 ligand (NA), 6 pockets (best druggability 0.84). MolNFT v1 #100179 on…
- PDB
- 4MPT
- Type
- protein
- Length
- 748 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative LEU/ILE/VAL-binding protein
- UniProt
- Q7VS30
- Ligands
- NA
- Pockets
- 6 · best druggability 0.84
Structure
x-ray diffraction · 1 distinct chain · 45% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Putative LEU/ILE/VAL-binding protein | protein | 374 | 45% helix, 21% strand | Q7VS30 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1132 | 0.84 | 0.85 | 107 | ACY |
| 2 | 54 | 0.64 | 0.94 | 19 | ACY |
| 3 | 60 | 0.61 | 0.91 | 18 | ACY |
| 4 | 69 | 0.32 | 0.75 | 18 | empty |
| 5 | 57 | 0.30 | 0.75 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 567 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 24 modified (engineered).
Compared structures
- 4MPT · Crystal Structure of Periplasmic binding Protein Type 1 from Bordetella pertussis Tohama I · 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 Q7VS30
- Elsewhere: RCSB PDB 4MPT · PDBe 4MPT · UniProt Q7VS30
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