Research workbench
Structure and function of the porb porin from disseminating N. gonorrhoeae
Analyse Structure and function of the porb porin from disseminating N. gonorrhoeae in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4AUI
- Type
- protein
- Length
- 947 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Porin (porb); Poly ala
- UniProt
- Q51056
- Ligands
- ATP, MG, PO4
- Pockets
- 18 · best druggability 0.72
Structure
x-ray diffraction · 3 distinct chains · 0% helix, 59% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Porin (porb) | protein | 308 | 0% helix, 61% strand | Q51056 |
| D, E | Poly ala | protein | 8 | 0% helix, 13% strand | — |
| F | Poly ala | protein | 7 | 0% helix, 29% strand | — |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 3 copies · chains A, B, C
- MG · Magnesium ion · metal · chains A
- PO4 · Phosphate ion · ion · 6 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 66 | 0.72 | 0.97 | 19 | empty |
| 2 | 53 | 0.70 | 0.98 | 23 | empty |
| 3 | 53 | 0.69 | 0.97 | 22 | empty |
| 4 | 52 | 0.69 | 0.97 | 22 | empty |
| 5 | 673 | 0.62 | 0.73 | 64 | ATP |
Interfaces
12 interfaces between chains.
- B–C · 1176 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 1160 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 1157 Ų buried · 6 hydrogen bonds · protein-protein
- A–D · 182 Ų buried · 0 hydrogen bonds · protein-protein
- D–F · 162 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 4AUI · Structure and function of the porb porin from disseminating N. gonorrhoeae · 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 Q51056
- Elsewhere: RCSB PDB 4AUI · PDBe 4AUI · UniProt Q51056
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.