MolNFT v1 · #184724 · protein
Crystal structure of helicobacter pylori comf fused to an artificial alpharep crystallization HELPER(NAMED B2)
7P0H · Helicobacter pylori comf fused to an artificial alpharep…: “Crystal structure of helicobacter pylori comf fused to an artificial alpharep crystallization HELPER(NAMED B2)”. X-ray diffraction, 3 ligands (PRP, MG, ZN), 20 pockets…
- 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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