Research workbench
Crystal structure of the outer membrane protein oprd from pseudomonas aeruginosa
Analyse Crystal structure of the outer membrane protein oprd from pseudomonas aeruginosa in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2ODJ
- Type
- protein
- Length
- 770 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Porin D
- EC
- 3.4.21.-
- UniProt
- P32722
- Pockets
- 6 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 1% helix, 57% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Porin D (EC 3.4.21.-) | protein | 382 | 0% helix, 56% strand | P32722 |
| B | Porin D (EC 3.4.21.-) | protein | 388 | 2% helix, 57% strand | P32722 |
Ligands and binding sites
- C8E · (hydroxyethyloxy)tri(ethyloxy)octane · additive · 8 copies · chains B, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 908 | 0.73 | 0.77 | 66 | C8E |
| 2 | 917 | 0.68 | 0.74 | 93 | empty |
| 3 | 695 | 0.65 | 0.75 | 90 | empty |
| 4 | 296 | 0.58 | 0.77 | 40 | empty |
| 5 | 293 | 0.56 | 0.76 | 34 | empty |
Interfaces
1 interface between chains.
- A–B · 252 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 modified (engineered).
Compared structures
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 P32722
- Elsewhere: RCSB PDB 2ODJ · PDBe 2ODJ · UniProt P32722
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