MolNFT v1 · #91758 · protein
Crystal structure of pseudomonas aeruginosa OCCK2 (opdf) in complex with glucuronate
4FMS · Probable porin: “Crystal structure of pseudomonas aeruginosa OCCK2 (opdf) in complex with glucuronate”. X-ray diffraction, 3 ligands (PGV, BDP, SO4), 9 pockets (best druggability 0.64). MolNFT v1 #91758 on GenesisL1: 3D structure…
- PDB
- 4FMS
- Type
- protein
- Length
- 737 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Probable porin
- UniProt
- Q9I6P8
- Ligands
- PGV, BDP, SO4
- Pockets
- 9 · best druggability 0.64
Structure
x-ray diffraction · 2 distinct chains · 1% helix, 64% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Probable porin | protein | 368 | 1% helix, 64% strand | Q9I6P8 |
| A | Probable porin | protein | 369 | 1% helix, 64% strand | Q9I6P8 |
Ligands and binding sites
- PGV · (1R)-2-{[{[(2S)-2,3-dihydroxypropyl]oxy}(hydroxy) phosphoryl]oxy}-1-[(palmitoyloxy)methyl]ethyl (11E)-octadec-11-enoate · ligand · 4 copies · chains B, A
- BDP · beta-D-glucopyranuronic acid · sugar · 2 copies · chains B, A
- SO4 · Sulfate ion · ion · 4 copies · chains B, A
- C8E · (hydroxyethyloxy)tri(ethyloxy)octane · additive · 7 copies · chains B, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 597 | 0.64 | 0.74 | 53 | C8E |
| 2 | 621 | 0.63 | 0.75 | 73 | BDP |
| 3 | 543 | 0.61 | 0.74 | 77 | BDP |
| 4 | 158 | 0.46 | 0.76 | 39 | empty |
| 5 | 128 | 0.38 | 0.73 | 21 | empty |
Interfaces
1 interface between chains.
- B–A · 206 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 4FMS · Crystal structure of Pseudomonas aeruginosa OccK2 (OpdF) in complex with glucuronate · the same entry in another collection · chain B against B, 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 Q9I6P8
- Elsewhere: RCSB PDB 4FMS · PDBe 4FMS · UniProt Q9I6P8
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