MolNFT v1 · #162570 · protein
Crystal structure of the wild type OMPK36 from klebsiella pneumonia
6RD3: “Crystal structure of the wild type OMPK36 from klebsiella pneumonia”. X-ray diffraction, 1 ligand (MG), 20 pockets (best druggability 0.82). MolNFT v1 #162570 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6RD3
- Type
- protein
- Length
- 2,064 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- OMPK36
- UniProt
- D6QLY0
- Ligands
- MG
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 3 distinct chains · 7% helix, 59% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | OMPK36 | protein | 342 | 6% helix, 59% strand | D6QLY0 |
| B, D, E, F | OMPK36 | protein | 345 | 9% helix, 59% strand | D6QLY0 |
| C | OMPK36 | protein | 342 | 7% helix, 59% strand | D6QLY0 |
Ligands and binding sites
- MG · Magnesium ion · metal · 6 copies · chains A, B, C, D, E, F
- C8E · (hydroxyethyloxy)tri(ethyloxy)octane · additive · 29 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, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 183 | 0.82 | 0.95 | 31 | empty |
| 2 | 169 | 0.81 | 0.95 | 24 | empty |
| 3 | 129 | 0.74 | 0.94 | 39 | empty |
| 4 | 135 | 0.74 | 0.93 | 46 | empty |
| 5 | 835 | 0.72 | 0.77 | 64 | empty |
Interfaces
7 interfaces between chains.
- D–F · 1709 Ų buried · 34 hydrogen bonds · protein-protein
- D–E · 1697 Ų buried · 30 hydrogen bonds · protein-protein
- A–B · 1696 Ų buried · 34 hydrogen bonds · protein-protein
- B–C · 1691 Ų buried · 28 hydrogen bonds · protein-protein
- A–C · 1685 Ų buried · 29 hydrogen bonds · protein-protein
Compared structures
- 6RD3 · Crystal structure of the wild type OmpK36 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 6RD3 · PDBe 6RD3 · UniProt D6QLY0
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