MolNFT v1 · #128674 · protein
Complex structure with maltose of providencia stuartii omp-PST1 porin
5NXU · Porin 1: “Complex structure with maltose of providencia stuartii omp-PST1 porin”. X-ray diffraction, 2 ligands (GLC, CA), 12 pockets (best druggability 0.86). MolNFT v1 #128674 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 5NXU
- Type
- protein
- Length
- 1,056 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Porin 1
- UniProt
- E3U904
- Ligands
- GLC, CA
- Pockets
- 12 · best druggability 0.86
Structure
x-ray diffraction · 1 distinct chain · 5% helix, 58% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Porin 1 | protein | 352 | 5% helix, 58% strand | E3U904 |
Ligands and binding sites
- GLC · alpha-D-glucopyranose · sugar · 6 copies · chains A, B, C
- CA · Calcium ion · metal · chains B, C
- LDA · Lauryl dimethylamine-N-oxide · additive · 19 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 632 | 0.86 | 0.90 | 49 | CA |
| 2 | 1030 | 0.76 | 0.79 | 75 | GLC |
| 3 | 952 | 0.75 | 0.78 | 65 | GLC |
| 4 | 1024 | 0.75 | 0.78 | 69 | GLC |
| 5 | 249 | 0.49 | 0.74 | 39 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1727 Ų buried · 37 hydrogen bonds · protein-protein
- B–C · 1708 Ų buried · 33 hydrogen bonds · protein-protein
- A–C · 1655 Ų buried · 31 hydrogen bonds · protein-protein
Compared structures
- 5NXU · Complex structure with maltose of Providencia stuartii Omp-Pst1 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 E3U904
- Elsewhere: RCSB PDB 5NXU · PDBe 5NXU · UniProt E3U904
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