Research workbench
Phospho-aspartyl intermediate analogue of ybiv from E. COLI K12
Analyse Phospho-aspartyl intermediate analogue of ybiv from E. COLI K12 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1RLO
- Type
- protein
- Length
- 1,072 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phosphatase
- EC
- 3.1.3.-
- UniProt
- P75792
- Ligands
- MG
- Pockets
- 9 · best druggability 0.75
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Phosphatase (EC 3.1.3.-) | protein | 268 | 39% helix, 24% strand | P75792 |
Ligands and binding sites
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
- GOL · Glycerol · additive · 2 copies · chains C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 594 | 0.75 | 0.82 | 88 | GOL |
| 2 | 424 | 0.63 | 0.77 | 60 | empty |
| 3 | 182 | 0.49 | 0.76 | 35 | empty |
| 4 | 99 | 0.45 | 0.80 | 20 | empty |
| 5 | 91 | 0.43 | 0.78 | 13 | empty |
Interfaces
3 interfaces between chains.
- C–D · 766 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 370 Ų buried · 8 hydrogen bonds · protein-protein
- A–D · 40 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (nonstandard).
Compared structures
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 P75792
- Elsewhere: RCSB PDB 1RLO · PDBe 1RLO · UniProt P75792
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