MolNFT v1 · #181111 · protein
The PILZ(DELTA107-117)-FIMX(GGDEF-eal) complex from xanthomonas citri
7LKQ: “The PILZ(DELTA107-117)-FIMX(GGDEF-eal) complex from xanthomonas citri”. X-ray diffraction, 3 ligands (C2E, MG, SO4), 2 pockets (best druggability 0.68). MolNFT v1 #181111 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7LKQ
- Type
- protein
- Length
- 347 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- FIMX(GGDEF-eal); Type IV fimbriae assembly protein
- UniProt
- Q8PJX9, Q8PND9
- Ligands
- C2E, MG, SO4
- Pockets
- 2 · best druggability 0.68
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | FIMX(GGDEF-eal) | protein | 254 | 47% helix, 21% strand | Q8PJX9 |
| B | Type IV fimbriae assembly protein | protein | 93 | 23% helix, 38% 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 · chains A, B
- MG · Magnesium ion · metal
- SO4 · Sulfate ion · ion · 5 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 612 | 0.68 | 0.77 | 49 | C2E |
| 2 | 225 | 0.63 | 0.82 | 22 | SO4 |
Interfaces
1 interface between chains.
- A–B · 805 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 7LKQ · The PilZ(delta107-117)-FimX(GGDEF-EAL) complex from Xanthomonas citri · 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 7LKQ · PDBe 7LKQ · UniProt Q8PJX9 · UniProt Q8PND9
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