Research workbench
Crystal structure of E. COLI HPPK(Y53A)
Analyse Crystal structure of E. COLI HPPK(Y53A) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3HSD
- Type
- protein
- Length
- 316 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hppk
- EC
- 2.7.6.3
- UniProt
- P26281
- Ligands
- MG, CL
- Pockets
- 5 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 33% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Hppk (EC 2.7.6.3) | protein | 158 | 33% helix, 26% strand | P26281 |
Ligands and binding sites
- MG · Magnesium ion · metal · 5 copies · chains A, B
- CL · Chloride ion · ion · 3 copies · chains A, B
- GOL · Glycerol · additive · 5 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 968 | 0.80 | 0.82 | 85 | MG, CL, GOL |
| 2 | 111 | 0.37 | 0.74 | 20 | MG, GOL |
| 3 | 72 | 0.31 | 0.74 | 14 | empty |
| 4 | 76 | 0.30 | 0.73 | 20 | CL |
| 5 | 53 | 0.27 | 0.74 | 11 | MG |
Interfaces
1 interface between chains.
- A–B · 796 Ų buried · 15 hydrogen bonds · protein-protein
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 P26281
- Elsewhere: RCSB PDB 3HSD · PDBe 3HSD · UniProt P26281
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