MolNFT v1 · #102691 · protein
Crystal structure of a putative lipoprotein (CD630_1653) from clostridium difficile 630 at 2.20 a resolution
4OTE: “Crystal structure of a putative lipoprotein (CD630_1653) from clostridium difficile 630 at 2.20 a resolution”. X-ray diffraction, 3 ligands (MSE, ZN, CL), 4 pockets (best druggability 0.72). MolNFT v1 #102691 on GenesisL1: 3D…
- PDB
- 4OTE
- Type
- protein
- Length
- 478 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lipoprotein
- UniProt
- Q186K7
- Ligands
- MSE, ZN, CL
- Pockets
- 4 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lipoprotein | protein | 238 | 41% helix, 24% strand | Q186K7 |
| B | Lipoprotein | protein | 240 | 41% helix, 23% strand | Q186K7 |
Ligands and binding sites
- MSE · Selenomethionine · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 15 copies · chains A, B
- CL · Chloride ion · ion · 6 copies · chains A, B
- ACT · Acetate ion · additive · 6 copies · chains A, B
- GOL · Glycerol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 497 | 0.72 | 0.81 | 58 | MSE, ACT |
| 2 | 467 | 0.72 | 0.81 | 63 | MSE, ACT |
| 3 | 67 | 0.37 | 0.78 | 14 | ACT |
| 4 | 55 | 0.27 | 0.73 | 12 | empty |
Interfaces
1 interface between chains.
- A–B · 430 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (engineered).
Compared structures
- 4OTE · Crystal structure of a putative lipoprotein (CD630_1653) from Clostridium difficile 630… · the same entry in another collection · chain B against B, 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 Q186K7
- Elsewhere: RCSB PDB 4OTE · PDBe 4OTE · UniProt Q186K7
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