Research workbench
X-ray crystal structure of a putative phosphate ABC transporter substrate-binding protein with bound phosphate from clostridium perfringens
Analyse X-ray crystal structure of a putative phosphate ABC transporter… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4GD5
- Type
- protein
- Length
- 486 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phosphate ABC transporter, phosphate-binding protein
- UniProt
- Q0TTH0
- Ligands
- CL, PO4
- Pockets
- 2 · best druggability 0.65
Structure
x-ray diffraction · 1 distinct chain · 37% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Phosphate ABC transporter, phosphate-binding protein | protein | 243 | 37% helix, 26% strand | Q0TTH0 |
Ligands and binding sites
- CL · Chloride ion · ion · 4 copies · chains A, B
- PO4 · Phosphate ion · ion · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · chains B
- PEG · Di(hydroxyethyl)ether · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 583 | 0.65 | 0.76 | 43 | PEG |
| 2 | 107 | 0.37 | 0.75 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 471 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 modified (engineered).
Compared structures
- 4GD5 · X-ray Crystal Structure of a Putative Phosphate ABC Transporter Substrate-Binding Protein… · 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 Q0TTH0
- Elsewhere: RCSB PDB 4GD5 · PDBe 4GD5 · UniProt Q0TTH0
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