Research workbench
Crystal structure of hoba (HP1230)FROM helicobacter pylori
Analyse Crystal structure of hoba (HP1230)FROM helicobacter pylori in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2UVP
- Type
- protein
- Length
- 723 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hoba
- UniProt
- O25828
- Ligands
- CA
- Pockets
- 11 · best druggability 0.72
Structure
x-ray diffraction · 4 distinct chains · 49% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hoba | protein | 180 | 49% helix, 15% strand | O25828 |
| B | Hoba | protein | 181 | 48% helix, 15% strand | O25828 |
| C | Hoba | protein | 186 | 47% helix, 14% strand | O25828 |
| D | Hoba | protein | 176 | 50% helix, 15% strand | O25828 |
Ligands and binding sites
- CA · Calcium ion · metal · 5 copies · chains B, C, D
- ACT · Acetate ion · additive · 3 copies · chains A, B, D, C
- GOL · Glycerol · additive · 2 copies · chains B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1028 | 0.72 | 0.76 | 106 | ACT |
| 2 | 69 | 0.72 | 0.97 | 16 | ACT |
| 3 | 69 | 0.72 | 0.97 | 17 | GOL |
| 4 | 1144 | 0.72 | 0.76 | 108 | ACT |
| 5 | 81 | 0.46 | 0.81 | 16 | GOL, CA |
Interfaces
4 interfaces between chains.
- A–B · 2200 Ų buried · 15 hydrogen bonds · protein-protein
- C–D · 2150 Ų buried · 14 hydrogen bonds · protein-protein
- B–C · 991 Ų buried · 12 hydrogen bonds · protein-protein
- A–D · 847 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 2UVP · Crystal structure of HobA (HP1230)from Helicobacter pylori · 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 O25828
- Elsewhere: RCSB PDB 2UVP · PDBe 2UVP · UniProt O25828
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