Research workbench
Crystal structure of ompf in complex with colicin peptide OBS1
Analyse Crystal structure of ompf in complex with colicin peptide OBS1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3O0E
- Type
- protein
- Length
- 2,123 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Porin ompf; Colicin-E9
- EC
- 3.1.-.-
- UniProt
- A0A418U3R0, P09883
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · 4 distinct chains · 4% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Porin ompf | protein | 340 | 4% helix, 59% strand | A0A418U3R0 |
| L | Colicin-E9 (EC 3.1.-.-) | protein | 14 | 0% helix, 0% strand | P09883 |
| M, N, P | Colicin-E9 (EC 3.1.-.-) | protein | 13 | 0% helix, 0% strand | P09883 |
| O, Q | Colicin-E9 (EC 3.1.-.-) | protein | 15 | 0% helix, 0% strand | P09883 |
Ligands and binding sites
- BOG · octyl beta-D-glucopyranoside · additive · 6 copies · chains B, F, A, C, D, 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, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 937 | 0.80 | 0.82 | 95 | empty |
| 2 | 898 | 0.79 | 0.81 | 99 | empty |
| 3 | 832 | 0.79 | 0.82 | 88 | empty |
| 4 | 1095 | 0.78 | 0.80 | 95 | empty |
| 5 | 1119 | 0.78 | 0.80 | 86 | empty |
Interfaces
17 interfaces between chains.
- C–E · 1571 Ų buried · 17 hydrogen bonds · protein-protein
- D–F · 1547 Ų buried · 17 hydrogen bonds · protein-protein
- B–F · 1520 Ų buried · 19 hydrogen bonds · protein-protein
- A–C · 1519 Ų buried · 18 hydrogen bonds · protein-protein
- B–D · 1512 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 3O0E · Crystal structure of OmpF in complex with colicin peptide OBS1 · the same entry in another collection · chain Q against Q, 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 A0A418U3R0
- Every structure of UniProt P09883
- Elsewhere: RCSB PDB 3O0E · PDBe 3O0E · UniProt A0A418U3R0 · UniProt P09883
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