Research workbench
Structure of porin omp-PST2 from P. stuartii; the asymmetric unit contains a dimer of trimers.
Analyse Structure of porin omp-PST2 from P. stuartii; the asymmetric unit contains a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4D65
- Type
- protein
- Length
- 2,058 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Porin 2
- UniProt
- E3U905
- Ligands
- FTT, MYR, SO4
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 1 distinct chain · 9% helix, 57% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Porin 2 | protein | 343 | 9% helix, 57% strand | E3U905 |
Ligands and binding sites
- FTT · 3-hydroxy-tetradecanoic acid · ligand · 6 copies · chains B, C, D
- MYR · Myristic acid · ligand · 6 copies · chains B, C, D
- SO4 · Sulfate ion · ion · 2 copies · chains A, B, C, D, E, F
- LDA · Lauryl dimethylamine-N-oxide · additive · 165 copies · chains A, C, B, D, F, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 875 | 0.83 | 0.85 | 60 | SO4 |
| 2 | 878 | 0.83 | 0.84 | 63 | SO4 |
| 3 | 998 | 0.75 | 0.78 | 75 | empty |
| 4 | 930 | 0.75 | 0.79 | 66 | empty |
| 5 | 981 | 0.75 | 0.78 | 73 | empty |
Interfaces
9 interfaces between chains.
- B–C · 1545 Ų buried · 26 hydrogen bonds · protein-protein
- A–C · 1538 Ų buried · 25 hydrogen bonds · protein-protein
- A–B · 1510 Ų buried · 25 hydrogen bonds · protein-protein
- D–E · 1506 Ų buried · 24 hydrogen bonds · protein-protein
- E–F · 1504 Ų buried · 25 hydrogen bonds · protein-protein
Compared structures
- 4D65 · Structure of porin Omp-Pst2 from P. stuartii; the asymmetric unit contains a dimer of… · 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 E3U905
- Elsewhere: RCSB PDB 4D65 · PDBe 4D65 · UniProt E3U905
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.