Research workbench
Structure of P. aeruginosa R1 pyocin fiber PALES_06171 comprising C- terminal residues 323-701
Analyse Structure of P. aeruginosa R1 pyocin fiber PALES_06171 comprising C- terminal… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6CL5
- Type
- protein
- Length
- 2,244 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tail fiber protein
- UniProt
- Q9KW03
- Ligands
- NA, FE, MG
- Pockets
- 11 · best druggability 0.87
Structure
x-ray diffraction · 1 distinct chain · 13% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Tail fiber protein | protein | 374 | 13% helix, 40% strand | Q9KW03 |
Ligands and binding sites
- NA · Sodium ion · metal · 6 copies · chains A, B, C, D, E, F
- FE · Fe (III) ion · metal · 2 copies · chains A, B, C, D, E, F
- MG · Magnesium ion · metal · 2 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 285 | 0.87 | 0.98 | 28 | empty |
| 2 | 280 | 0.87 | 0.98 | 27 | empty |
| 3 | 217 | 0.84 | 0.96 | 32 | empty |
| 4 | 205 | 0.82 | 0.95 | 32 | empty |
| 5 | 113 | 0.82 | 0.99 | 18 | empty |
Interfaces
10 interfaces between chains.
- B–C · 5730 Ų buried · 86 hydrogen bonds · protein-protein
- A–B · 5701 Ų buried · 85 hydrogen bonds · protein-protein
- E–F · 5701 Ų buried · 85 hydrogen bonds · protein-protein
- A–C · 5675 Ų buried · 87 hydrogen bonds · protein-protein
- D–E · 5672 Ų buried · 90 hydrogen bonds · protein-protein
Compared structures
- 6CL5 · Structure of P. aeruginosa R1 pyocin fiber PALES_06171 comprising C-terminal residues… · 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 Q9KW03
- Elsewhere: RCSB PDB 6CL5 · PDBe 6CL5 · UniProt Q9KW03
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