Research workbench
Crystal structure of bifidobacterium longum multiple inositol polyphosphate phosphatase apo form
Analyse Crystal structure of bifidobacterium longum multiple inositol polyphosphate… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6RXD
- Type
- protein
- Length
- 1,018 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histidine acid phosphatase
- UniProt
- B7GTV0
- Ligands
- ZN
- Pockets
- 8 · best druggability 0.75
Structure
x-ray diffraction · 1 distinct chain · 46% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Histidine acid phosphatase | protein | 509 | 46% helix, 13% strand | B7GTV0 |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 926 | 0.75 | 0.78 | 87 | empty |
| 2 | 969 | 0.74 | 0.77 | 91 | empty |
| 3 | 479 | 0.62 | 0.76 | 47 | empty |
| 4 | 403 | 0.59 | 0.76 | 49 | empty |
| 5 | 104 | 0.36 | 0.74 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 941 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 6RXD · Crystal Structure of Bifidobacterium longum Multiple Inositol Polyphosphate Phosphatase… · 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 B7GTV0
- Elsewhere: RCSB PDB 6RXD · PDBe 6RXD · UniProt B7GTV0
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