Research workbench
Structure of the pilz-FIMX(EAL domain)-C-di-gmp complex responsible for the regulation of bacterial type IV pilus biogenesis
Analyse Structure of the pilz-FIMX(EAL domain)-C-di-gmp complex responsible for the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4FOU
- Type
- protein
- Length
- 713 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fimx; Type IV fimbriae assembly protein
- UniProt
- Q8PJX9, Q8PND9
- Ligands
- C2E, CA
- Pockets
- 5 · best druggability 0.80
Structure
x-ray diffraction · 4 distinct chains · 42% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Fimx | protein | 262 | 48% helix, 20% strand | Q8PJX9 |
| B | Fimx | protein | 261 | 49% helix, 20% strand | Q8PJX9 |
| D | Type IV fimbriae assembly protein | protein | 95 | 23% helix, 37% strand | Q8PND9 |
| C | Type IV fimbriae assembly protein | protein | 95 | 22% helix, 37% strand | Q8PND9 |
Ligands and binding sites
- C2E · 9,9'-[(2r,3r,3as,5s,7ar,9r,10r,10as,12s,14ar)-3,5,10, 12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3, 2-D:3',2'-J][1,3,7,9,2, 8]tetraoxadiphosphacyclododecine-2,9-diyl]bis(2-amino-1,9-dihydro-6H-purin-6-one) · ligand · 2 copies · chains A, C, B
- CA · Calcium ion · metal · 3 copies · chains A, B, C
- GOL · Glycerol · additive · 3 copies · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 885 | 0.80 | 0.82 | 93 | C2E |
| 2 | 607 | 0.77 | 0.83 | 52 | CA |
| 3 | 82 | 0.70 | 0.94 | 16 | CA |
| 4 | 678 | 0.68 | 0.76 | 67 | C2E |
| 5 | 134 | 0.48 | 0.78 | 21 | empty |
Interfaces
5 interfaces between chains.
- A–C · 935 Ų buried · 11 hydrogen bonds · protein-protein
- B–D · 806 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 733 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 582 Ų buried · 13 hydrogen bonds · protein-protein
- D–C · 78 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4FOU · Structure of the PilZ-FimX(EAL domain)-c-di-GMP complex responsible for the regulation of… · 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 Q8PJX9
- Every structure of UniProt Q8PND9
- Elsewhere: RCSB PDB 4FOU · PDBe 4FOU · UniProt Q8PJX9 · UniProt Q8PND9
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