Research workbench
Crystal structure of putative membrane protein from clostridium difficile 630
Analyse Crystal structure of putative membrane protein from clostridium difficile 630 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3KMI
- Type
- protein
- Length
- 340 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative membrane protein COG4129
- UniProt
- Q184N1
- Pockets
- 6 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 80% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative membrane protein COG4129 | protein | 172 | 81% helix, 0% strand | Q184N1 |
| B | Putative membrane protein COG4129 | protein | 168 | 79% helix, 0% strand | Q184N1 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 624 | 0.72 | 0.79 | 76 | empty |
| 2 | 221 | 0.52 | 0.77 | 24 | empty |
| 3 | 70 | 0.40 | 0.79 | 16 | EDO, FMT |
| 4 | 109 | 0.40 | 0.76 | 12 | empty |
| 5 | 56 | 0.33 | 0.78 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 1395 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 modified (engineered).
Compared structures
- 3KMI · Crystal structure of putative membrane protein from Clostridium difficile 630 · 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 Q184N1
- Elsewhere: RCSB PDB 3KMI · PDBe 3KMI · UniProt Q184N1
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