Research workbench
Crystal structure of novel amino acid binding protein from shigella flexneri
Analyse Crystal structure of novel amino acid binding protein from shigella flexneri in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2IA4
- Type
- protein
- Length
- 555 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative periplasmic binding transport protein
- UniProt
- Q83S74
- Ligands
- GLU
- Pockets
- 5 · best druggability 0.48
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative periplasmic binding transport protein | protein | 277 | 37% helix, 24% strand | Q83S74 |
| B | Putative periplasmic binding transport protein | protein | 278 | 37% helix, 24% strand | Q83S74 |
Ligands and binding sites
- GLU · Glutamic acid · ligand · 2 copies · chains A, B
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 184 | 0.48 | 0.76 | 24 | empty |
| 2 | 88 | 0.32 | 0.73 | 18 | empty |
| 3 | 71 | 0.31 | 0.74 | 16 | empty |
| 4 | 62 | 0.31 | 0.75 | 14 | empty |
| 5 | 67 | 0.28 | 0.73 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 752 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 modified, 2 disulfide (engineered, disulfide).
Compared structures
- 2IA4 · Crystal structure of Novel amino acid binding protein from Shigella flexneri · 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 Q83S74
- Elsewhere: RCSB PDB 2IA4 · PDBe 2IA4 · UniProt Q83S74
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