Research workbench
Structure of a domain from the type IV pilus biogenesis lipoprotein pilp, from pseudomonas aeruginosa
Analyse Structure of a domain from the type IV pilus biogenesis lipoprotein pilp, from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2Y4Y
- Type
- protein
- Length
- 317 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pilp protein
- UniProt
- Q51354
- Ligands
- ZN
- Pockets
- 7 · best druggability 0.45
Structure
x-ray diffraction · 4 distinct chains · 9% helix, 56% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pilp protein | protein | 82 | 9% helix, 52% strand | Q51354 |
| B | Pilp protein | protein | 76 | 9% helix, 58% strand | Q51354 |
| C | Pilp protein | protein | 79 | 9% helix, 56% strand | Q51354 |
| D | Pilp protein | protein | 80 | 9% helix, 58% strand | Q51354 |
Ligands and binding sites
- ZN · Zinc ion · metal · 6 copies · chains A, C, B, D
- ACT · Acetate ion · additive · 6 copies · chains A, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 170 | 0.45 | 0.75 | 35 | empty |
| 2 | 123 | 0.45 | 0.77 | 18 | empty |
| 3 | 123 | 0.41 | 0.75 | 18 | empty |
| 4 | 114 | 0.40 | 0.75 | 15 | empty |
| 5 | 73 | 0.32 | 0.74 | 13 | ACT |
Interfaces
3 interfaces between chains.
- A–C · 368 Ų buried · 4 hydrogen bonds · protein-protein
- A–D · 359 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 342 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 2Y4Y · Structure of a domain from the type IV pilus biogenesis lipoprotein PilP, from… · 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 Q51354
- Elsewhere: RCSB PDB 2Y4Y · PDBe 2Y4Y · UniProt Q51354
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