MolNFT v1 · #128959 · protein
Crystal structure of the pseudomonas functional amyloid secretion protein fapf
5O65: “Crystal structure of the pseudomonas functional amyloid secretion protein fapf”. X-ray diffraction, 1 ligand (NA), 13 pockets (best druggability 0.79). MolNFT v1 #128959 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5O65
- Type
- protein
- Length
- 850 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fapf
- UniProt
- C4IN73
- Ligands
- NA
- Pockets
- 13 · best druggability 0.79
Structure
x-ray diffraction · 3 distinct chains · 4% helix, 60% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Fapf | protein | 276 | 4% helix, 61% strand | C4IN73 |
| B | Fapf | protein | 296 | 4% helix, 58% strand | C4IN73 |
| C | Fapf | protein | 278 | 4% helix, 61% strand | C4IN73 |
Ligands and binding sites
- NA · Sodium ion · metal · 3 copies · chains A, C, B
- LDA · Lauryl dimethylamine-N-oxide · additive · 7 copies · chains A, B, C
- C8E · (hydroxyethyloxy)tri(ethyloxy)octane · additive · 6 copies · chains A, C, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1052 | 0.79 | 0.81 | 86 | LDA |
| 2 | 979 | 0.79 | 0.81 | 87 | LDA |
| 3 | 1052 | 0.78 | 0.80 | 89 | LDA |
| 4 | 506 | 0.68 | 0.78 | 57 | LDA |
| 5 | 472 | 0.67 | 0.78 | 53 | C8E |
Interfaces
3 interfaces between chains.
- A–B · 951 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 928 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 865 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 modified (engineered).
Compared structures
- 5O65 · Crystal Structure of the Pseudomonas functional amyloid secretion protein FapF · 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 C4IN73
- Elsewhere: RCSB PDB 5O65 · PDBe 5O65 · UniProt C4IN73
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