Research workbench
Crystal structure of helicobacter pylori comf fused to an artificial alpharep crystallization HELPER(NAMED B2)
Analyse Crystal structure of helicobacter pylori comf fused to an artificial alpharep… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7P0H
- Type
- protein
- Length
- 1,644 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Helicobacter pylori comf fused to an artificial alpharep crystallization helper (named B2)
- UniProt
- O26008
- Ligands
- PRP, MG, ZN
- Pockets
- 20 · best druggability 0.77
Structure
x-ray diffraction · 1 distinct chain · 57% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Helicobacter pylori comf fused to an artificial alpharep crystallization helper (named B2) | protein | 411 | 57% helix, 13% strand | O26008 |
Ligands and binding sites
- PRP · 1-O-pyrophosphono-5-O-phosphono-alpha-D-ribofuranose · ligand · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 8 copies · chains A, B, C, D
- ZN · Zinc ion · metal · 4 copies · chains A, B, C, D
- GOL · Glycerol · additive · 14 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 469 | 0.77 | 0.85 | 45 | PRP, MG |
| 2 | 418 | 0.74 | 0.84 | 41 | PRP, MG |
| 3 | 442 | 0.73 | 0.83 | 45 | PRP, MG |
| 4 | 426 | 0.73 | 0.83 | 41 | PRP, MG |
| 5 | 256 | 0.68 | 0.84 | 35 | GOL |
Interfaces
4 interfaces between chains.
- A–C · 2845 Ų buried · 34 hydrogen bonds · protein-protein
- B–D · 2825 Ų buried · 32 hydrogen bonds · protein-protein
- A–D · 319 Ų buried · 0 hydrogen bonds · protein-protein
- B–C · 314 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 modified (engineered).
Compared structures
- 7P0H · Crystal structure of Helicobacter pylori ComF fused to an artificial alphaREP… · 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 O26008
- Elsewhere: RCSB PDB 7P0H · PDBe 7P0H · UniProt O26008
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