Research workbench
Crystal structure of P. aeruginosa pilt with bound AMP-pcp
Analyse Crystal structure of P. aeruginosa pilt with bound AMP-pcp in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3JVV
- Type
- protein
- Length
- 996 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Twitching mobility protein
- UniProt
- P24559
- Ligands
- ACP, MG
- Pockets
- 9 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 39% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Twitching mobility protein | protein | 331 | 39% helix, 27% strand | P24559 |
| B | Twitching mobility protein | protein | 328 | 39% helix, 26% strand | P24559 |
| C | Twitching mobility protein | protein | 337 | 38% helix, 28% strand | P24559 |
Ligands and binding sites
- ACP · Phosphomethylphosphonic acid adenylate ester · ligand · 3 copies · chains A, B, C
- MG · Magnesium ion · metal · 3 copies · chains A, B, C
- CIT · Citric acid · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 999 | 0.81 | 0.83 | 78 | ACP, MG |
| 2 | 717 | 0.80 | 0.85 | 72 | ACP, MG |
| 3 | 301 | 0.74 | 0.86 | 40 | empty |
| 4 | 493 | 0.72 | 0.81 | 57 | empty |
| 5 | 443 | 0.64 | 0.78 | 57 | ACP, MG |
Interfaces
2 interfaces between chains.
- A–B · 1575 Ų buried · 35 hydrogen bonds · protein-protein
- B–C · 1558 Ų buried · 33 hydrogen bonds · protein-protein
Compared structures
- 3JVV · Crystal Structure of P. aeruginosa PilT with bound AMP-PCP · the same entry in another collection · chain A against A, TM-score 1.00
- P24559 · AlphaFold monomer V2.0 prediction for type IV pilus retractation ATPase pilt (P24559) · a predicted model of the same protein · chain B against A, TM-score 0.97
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 P24559
- Elsewhere: RCSB PDB 3JVV · PDBe 3JVV · UniProt P24559
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