Research workbench
Crystal structure of the OMPK36 td insertion chimera from klebsiella pneumonia
Analyse Crystal structure of the OMPK36 td insertion chimera from klebsiella pneumonia in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7PZF
- Type
- protein
- Length
- 2,078 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- OMPK36
- UniProt
- D6QLY0
- Ligands
- C14, LI
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 8% helix, 59% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, F | OMPK36 | protein | 347 | 8% helix, 60% strand | D6QLY0 |
| E | OMPK36 | protein | 343 | 8% helix, 59% strand | D6QLY0 |
Ligands and binding sites
- C14 · Tetradecane · ligand · 21 copies · chains A, C, B, F, D, E
- LI · Lithium ion · metal · 9 copies · chains A, 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, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 188 | 0.83 | 0.96 | 30 | empty |
| 2 | 188 | 0.82 | 0.96 | 27 | empty |
| 3 | 778 | 0.76 | 0.80 | 69 | C14 |
| 4 | 138 | 0.75 | 0.94 | 46 | empty |
| 5 | 144 | 0.75 | 0.93 | 45 | empty |
Interfaces
7 interfaces between chains.
- A–B · 1716 Ų buried · 31 hydrogen bonds · protein-protein
- A–C · 1711 Ų buried · 33 hydrogen bonds · protein-protein
- D–E · 1701 Ų buried · 35 hydrogen bonds · protein-protein
- E–F · 1696 Ų buried · 31 hydrogen bonds · protein-protein
- D–F · 1667 Ų buried · 33 hydrogen bonds · protein-protein
Compared structures
- 7PZF · Crystal structure of the OmpK36 TD insertion chimera from Klebsiella pneumonia · 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 D6QLY0
- Elsewhere: RCSB PDB 7PZF · PDBe 7PZF · UniProt D6QLY0
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