MolNFT v1 · #75398 · protein
Crystal structure of E.COLI ompf porin in lipidic cubic phase: space group P1
3POX · Ompf protein: “Crystal structure of E.COLI ompf porin in lipidic cubic phase: space group P1”. X-ray diffraction, 2 ligands (K, SCN), 20 pockets (best druggability 0.71). MolNFT v1 #75398 on GenesisL1: 3D structure, binding sites…
- PDB
- 3POX
- Type
- protein
- Length
- 2,040 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ompf protein
- UniProt
- C5W2U9
- Ligands
- K, SCN
- Pockets
- 20 · best druggability 0.71
Structure
x-ray diffraction · 1 distinct chain · 4% helix, 59% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Ompf protein | protein | 340 | 4% helix, 59% strand | C5W2U9 |
Ligands and binding sites
- K · Potassium ion · metal · 20 copies · chains A, B, C, D, E, F
- SCN · Thiocyanate ion · ion · 6 copies · chains A, B, D, E, F
- OLC · (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate · additive · 88 copies · chains A, C, B, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1027 | 0.71 | 0.75 | 73 | empty |
| 2 | 1006 | 0.70 | 0.75 | 67 | empty |
| 3 | 1017 | 0.70 | 0.74 | 70 | SCN |
| 4 | 1057 | 0.70 | 0.74 | 74 | SCN |
| 5 | 1075 | 0.70 | 0.74 | 67 | SCN |
Interfaces
7 interfaces between chains.
- B–C · 1503 Ų buried · 16 hydrogen bonds · protein-protein
- D–F · 1497 Ų buried · 16 hydrogen bonds · protein-protein
- E–F · 1493 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 1486 Ų buried · 17 hydrogen bonds · protein-protein
- D–E · 1484 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 3POX · Crystal Structure of E.coli OmpF porin in lipidic cubic phase: space group P1 · 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 C5W2U9
- Elsewhere: RCSB PDB 3POX · PDBe 3POX · UniProt C5W2U9
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