Research workbench
X-ray crystal structure of enterobacter cloacae OMPE36 porin
Analyse X-ray crystal structure of enterobacter cloacae OMPE36 porin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5FVN
- Type
- protein
- Length
- 2,052 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ompc porin
- UniProt
- Q93K99
- Ligands
- FTT, DAO, GP1, Z9M, MYR, KDO, GMH, CA, PO4, SO4
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 8% helix, 59% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Ompc porin | protein | 342 | 8% helix, 59% strand | Q93K99 |
Ligands and binding sites
- FTT · 3-hydroxy-tetradecanoic acid · ligand · 36 copies · chains A, B, C, D, E, F
- DAO · Lauric acid · ligand · 15 copies · chains A, C, D, E
- GP1 · 2-amino-2-deoxy-1-O-phosphono-alpha-D-glucopyranose · ligand · 9 copies · chains A, B, C, D, E, F
- Z9M · 2-amino-2-deoxy-4-O-phosphono-beta-D-glucopyranose · ligand · 9 copies · chains A, B, C, D, E, F
- MYR · Myristic acid · ligand · 9 copies · chains A, B, C, D, E, F
- KDO · 3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid · sugar · 17 copies · chains A, B, C, D, E, F
- GMH · L-glycero-alpha-D-manno-heptopyranose · sugar · 3 copies · chains B
- CA · Calcium ion · metal · 2 copies · chains C, F
- PO4 · Phosphate ion · ion · 6 copies · chains A, B, C, D, E, F
- SO4 · Sulfate ion · ion · 2 copies · chains A, B, C, D, E, F
- C8E · (hydroxyethyloxy)tri(ethyloxy)octane · additive · 37 copies · chains A, B, C, 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 | 706 | 0.82 | 0.86 | 30 | empty |
| 2 | 903 | 0.73 | 0.77 | 66 | PO4 |
| 3 | 881 | 0.73 | 0.78 | 76 | PO4 |
| 4 | 1070 | 0.72 | 0.76 | 72 | PO4 |
| 5 | 1146 | 0.72 | 0.76 | 75 | C8E, PO4 |
Interfaces
12 interfaces between chains.
- E–F · 1672 Ų buried · 31 hydrogen bonds · protein-protein
- A–C · 1658 Ų buried · 31 hydrogen bonds · protein-protein
- B–C · 1654 Ų buried · 31 hydrogen bonds · protein-protein
- D–F · 1648 Ų buried · 30 hydrogen bonds · protein-protein
- D–E · 1639 Ų buried · 31 hydrogen bonds · protein-protein
Compared structures
- 5FVN · X-ray crystal structure of Enterobacter cloacae OmpE36 porin. · 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 Q93K99
- Elsewhere: RCSB PDB 5FVN · PDBe 5FVN · UniProt Q93K99
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