MolNFT v1 · #118001 · protein
Pseudomonas aeruginosa semet-pilm bound to ADP
5EOY · Type 4 fimbrial biogenesis protein pilm: “Pseudomonas aeruginosa semet-pilm bound to ADP”. X-ray diffraction, 2 ligands (ADP, MG), 7 pockets (best druggability 0.76). MolNFT v1 #118001 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5EOY
- Type
- protein
- Length
- 710 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Type 4 fimbrial biogenesis protein pilm
- UniProt
- G3XD28
- Ligands
- ADP, MG
- Pockets
- 7 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Type 4 fimbrial biogenesis protein pilm | protein | 356 | 40% helix, 29% strand | G3XD28 |
| B | Type 4 fimbrial biogenesis protein pilm | protein | 354 | 41% helix, 29% strand | G3XD28 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 3 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, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 768 | 0.76 | 0.81 | 73 | ADP, MG |
| 2 | 746 | 0.75 | 0.80 | 79 | ADP, MG |
| 3 | 302 | 0.58 | 0.77 | 32 | empty |
| 4 | 292 | 0.56 | 0.77 | 28 | empty |
| 5 | 210 | 0.54 | 0.78 | 32 | empty |
Interfaces
1 interface between chains.
- A–B · 1715 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 modified (engineered).
Compared structures
- 5EOY · Pseudomonas aeruginosa SeMet-PilM bound to ADP · 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 B against A, TM-score 0.94
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
- Elsewhere: RCSB PDB 5EOY · PDBe 5EOY · UniProt G3XD28
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