MolNFT v1 · #84175 · protein
Crystal structure of helicobacter pylori T4SS protein cagl in a tetragonal crystal form with a helical rgd-motif (6 mol per asu)
3ZCJ: “Crystal structure of helicobacter pylori T4SS protein cagl in a tetragonal crystal form with a helical…”. X-ray diffraction, 2 ligands (K, PO4), 16 pockets (best druggability 0.77). MolNFT v1 #84175 on GenesisL1: 3D structure…
- PDB
- 3ZCJ
- Type
- protein
- Length
- 1,142 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cagl
- UniProt
- O25272
- Ligands
- K, PO4
- Pockets
- 16 · best druggability 0.77
Structure
x-ray diffraction · 6 distinct chains · 88% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cagl | protein | 205 | 90% helix, 0% strand | O25272 |
| B | Cagl | protein | 199 | 85% helix, 0% strand | O25272 |
| C | Cagl | protein | 185 | 88% helix, 0% strand | O25272 |
| D | Cagl | protein | 194 | 87% helix, 0% strand | O25272 |
| E | Cagl | protein | 193 | 88% helix, 0% strand | O25272 |
| F | Cagl | protein | 166 | 91% helix, 0% strand | O25272 |
Ligands and binding sites
- K · Potassium ion · metal · chains D
- PO4 · Phosphate ion · ion · 2 copies · chains B, F
- GOL · Glycerol · additive · 8 copies · chains A, B, C, D, E, F
- PEG · Di(hydroxyethyl)ether · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 947 | 0.77 | 0.79 | 103 | PEG, GOL |
| 2 | 617 | 0.71 | 0.78 | 54 | GOL |
| 3 | 619 | 0.67 | 0.76 | 50 | empty |
| 4 | 490 | 0.67 | 0.78 | 46 | GOL |
| 5 | 536 | 0.63 | 0.75 | 54 | GOL |
Interfaces
8 interfaces between chains.
- A–B · 1044 Ų buried · 1 hydrogen bond · protein-protein
- C–F · 441 Ų buried · 1 hydrogen bond · protein-protein
- A–C · 437 Ų buried · 4 hydrogen bonds · protein-protein
- D–E · 411 Ų buried · 3 hydrogen bonds · protein-protein
- B–E · 402 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 107 modified, 4 disulfide (methylation, disulfide).
Compared structures
- 3ZCJ · Crystal structure of Helicobacter pylori T4SS protein CagL in a tetragonal crystal form… · 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 O25272
- Elsewhere: RCSB PDB 3ZCJ · PDBe 3ZCJ · UniProt O25272
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