Research workbench
Crystal structure of the OMPK36 gd insertion chimera from klebsiella pneumonia
Analyse Crystal structure of the OMPK36 gd 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
- 6RCK
- Type
- protein
- Length
- 1,038 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- OMPK36
- UniProt
- D6QLY1
- Ligands
- P6L
- Pockets
- 11 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 8% helix, 60% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | OMPK36 | protein | 344 | 8% helix, 60% strand | D6QLY1 |
| B, C | OMPK36 | protein | 347 | 8% helix, 60% strand | D6QLY1 |
Ligands and binding sites
- P6L · (2S)-3-{[{[(2S)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-2-[(6E)-hexadec-6-enoyloxy]propyl (8E)-octadec-8-enoate · ligand · chains C
- C8E · (hydroxyethyloxy)tri(ethyloxy)octane · additive · 8 copies · chains A, C, B
- LDA · Lauryl dimethylamine-N-oxide · additive · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 183 | 0.83 | 0.96 | 30 | empty |
| 2 | 1104 | 0.72 | 0.76 | 74 | empty |
| 3 | 1140 | 0.72 | 0.76 | 84 | empty |
| 4 | 1109 | 0.72 | 0.76 | 77 | empty |
| 5 | 100 | 0.71 | 0.93 | 27 | empty |
Interfaces
3 interfaces between chains.
- B–C · 1653 Ų buried · 30 hydrogen bonds · protein-protein
- A–C · 1642 Ų buried · 31 hydrogen bonds · protein-protein
- A–B · 1623 Ų buried · 30 hydrogen bonds · protein-protein
Compared structures
- 6RCK · Crystal structure of the OmpK36 GD 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 D6QLY1
- Elsewhere: RCSB PDB 6RCK · PDBe 6RCK · UniProt D6QLY1
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