MolNFT v1 · #138975 · protein
Crystal structure of flim-spee complex from H. pylori
5X0Z · Polyamine aminopropyltransferase: “Crystal structure of flim-spee complex from H. pylori”. X-ray diffraction, 15 pockets (best druggability 0.81). MolNFT v1 #138975 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5X0Z
- Type
- protein
- Length
- 1,416 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Polyamine aminopropyltransferase; Flagellar motor switch protein (flim)
- EC
- 2.5.1.22, 2.5.1.16
- UniProt
- O25503, O25675
- Pockets
- 15 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 36% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Polyamine aminopropyltransferase (EC 2.5.1.22, 2.5.1.16) | protein | 262 | 29% helix, 31% strand | O25503 |
| E | Flagellar motor switch protein (flim) | protein | 185 | 41% helix, 28% strand | O25675 |
| F | Flagellar motor switch protein (flim) | protein | 183 | 40% helix, 29% strand | O25675 |
Ligands and binding sites
- FLC · Citrate anion · additive · chains A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 992 | 0.81 | 0.82 | 89 | empty |
| 2 | 155 | 0.78 | 0.95 | 34 | FLC |
| 3 | 522 | 0.78 | 0.85 | 66 | empty |
| 4 | 418 | 0.75 | 0.85 | 54 | empty |
| 5 | 81 | 0.75 | 0.97 | 27 | empty |
Interfaces
10 interfaces between chains.
- C–D · 1756 Ų buried · 29 hydrogen bonds · protein-protein
- A–B · 1747 Ų buried · 29 hydrogen bonds · protein-protein
- A–D · 1003 Ų buried · 8 hydrogen bonds · protein-protein
- B–E · 735 Ų buried · 23 hydrogen bonds · protein-protein
- C–F · 722 Ų buried · 23 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 O25503
- Every structure of UniProt O25675
- Elsewhere: RCSB PDB 5X0Z · PDBe 5X0Z · UniProt O25503 · UniProt O25675
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