Research workbench
Pseudomonas aeruginosa PILM:PILN1-12 bound to ATP
Analyse Pseudomonas aeruginosa PILM:PILN1-12 bound to ATP in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5EOU
- Type
- protein
- Length
- 685 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Type 4 fimbrial biogenesis protein PILM,TYPE 4 fimbrial biogenesis protein piln
- UniProt
- G3XD28, G3XD30
- Ligands
- ATP, NA, MG, SO4, CL
- Pockets
- 7 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Type 4 fimbrial biogenesis protein PILM,TYPE 4 fimbrial biogenesis protein piln | protein | 333 | 35% helix, 29% strand | G3XD28, G3XD30 |
| B | Type 4 fimbrial biogenesis protein PILM,TYPE 4 fimbrial biogenesis protein piln | protein | 352 | 40% helix, 29% strand | G3XD28, G3XD30 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · chains B
- NA · Sodium ion · metal · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 8 copies · chains A, B
- CL · Chloride ion · ion · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 724 | 0.73 | 0.79 | 82 | ATP, CL, MG |
| 2 | 663 | 0.71 | 0.78 | 69 | SO4, MG |
| 3 | 470 | 0.64 | 0.77 | 74 | SO4, CL |
| 4 | 91 | 0.36 | 0.75 | 18 | empty |
| 5 | 57 | 0.33 | 0.77 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 513 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 5EOU · Pseudomonas aeruginosa PilM:PilN1-12 bound to ATP · the same entry in another collection · chain A against A, TM-score 1.00
- G3XD28 · AlphaFold monomer V2.0 prediction for type IV pilus inner membrane component pilm (G3XD28) · a predicted model of the same protein · chain A against A, TM-score 0.94
- G3XD30 · AlphaFold monomer V2.0 prediction for type IV pilus inner membrane component piln (G3XD30) · a predicted model of the same protein · chain A against A, TM-score 0.16
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 G3XD28
- Every structure of UniProt G3XD30
- Elsewhere: RCSB PDB 5EOU · PDBe 5EOU · UniProt G3XD28 · UniProt G3XD30
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.