Research workbench
Crystal structure of putative lipoprotein from peptoclostridium difficile 630 (fragment)
Analyse Crystal structure of putative lipoprotein from peptoclostridium difficile 630… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4YCS
- Type
- protein
- Length
- 734 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uncharacterized protein
- UniProt
- A0A031WBX8
- Ligands
- NA
- Pockets
- 5 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Uncharacterized protein | protein | 123 | 45% helix, 24% strand | A0A031WBX8 |
| C, D, E, F | Uncharacterized protein | protein | 122 | 45% helix, 25% strand | A0A031WBX8 |
Ligands and binding sites
- NA · Sodium ion · metal · chains D, E
- GOL · Glycerol · additive · 3 copies · chains A, C, E, D
- ACT · Acetate ion · additive · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1173 | 0.77 | 0.80 | 120 | NA, GOL |
| 2 | 153 | 0.44 | 0.75 | 30 | empty |
| 3 | 85 | 0.34 | 0.75 | 22 | empty |
| 4 | 52 | 0.32 | 0.77 | 13 | empty |
| 5 | 70 | 0.31 | 0.75 | 13 | empty |
Interfaces
7 interfaces between chains.
- B–C · 575 Ų buried · 13 hydrogen bonds · protein-protein
- D–E · 558 Ų buried · 13 hydrogen bonds · protein-protein
- A–F · 509 Ų buried · 10 hydrogen bonds · protein-protein
- C–E · 431 Ų buried · 12 hydrogen bonds · protein-protein
- E–F · 279 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 24 modified (engineered).
Compared structures
- 4YCS · Crystal structure of putative lipoprotein from Peptoclostridium difficile 630 (fragment) · the same entry in another collection · chain D against D, 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 A0A031WBX8
- Elsewhere: RCSB PDB 4YCS · PDBe 4YCS · UniProt A0A031WBX8
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