Research workbench
Crystal structure of the oprm channel in a non-symmetrical space group
Analyse Crystal structure of the oprm channel in a non-symmetrical space group in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3D5K
- Type
- protein
- Length
- 1,365 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Outer membrane protein oprm
- UniProt
- Q51487
- Ligands
- NA, CL
- Pockets
- 20 · best druggability 0.75
Structure
x-ray diffraction · 1 distinct chain · 60% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Outer membrane protein oprm | protein | 455 | 60% helix, 13% strand | Q51487 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1134 | 0.75 | 0.77 | 76 | empty |
| 2 | 239 | 0.53 | 0.77 | 43 | empty |
| 3 | 209 | 0.48 | 0.75 | 42 | empty |
| 4 | 201 | 0.46 | 0.74 | 31 | empty |
| 5 | 167 | 0.44 | 0.75 | 31 | empty |
Interfaces
3 interfaces between chains.
- A–B · 2843 Ų buried · 33 hydrogen bonds · protein-protein
- A–C · 2837 Ų buried · 40 hydrogen bonds · protein-protein
- B–C · 2822 Ų buried · 34 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 modified (acetylation).
Compared structures
- 3D5K · Crystal structure of the OprM channel in a non-symmetrical space group · the same entry in another collection · chain A against A, TM-score 1.00
- Q51487 · AlphaFold monomer V2.0 prediction for outer membrane protein oprm (Q51487) · a predicted model of the same protein · chain A against A, TM-score 0.95
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 Q51487
- Elsewhere: RCSB PDB 3D5K · PDBe 3D5K · UniProt Q51487
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