Research workbench
Crystal structure of the fapf polypeptide transporter - F103A mutant
Analyse Crystal structure of the fapf polypeptide transporter - F103A mutant in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5O67
- Type
- protein
- Length
- 857 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fapf
- UniProt
- C4IN73
- Pockets
- 14 · best druggability 0.78
Structure
x-ray diffraction · 3 distinct chains · 4% helix, 59% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Fapf | protein | 282 | 4% helix, 59% strand | C4IN73 |
| B | Fapf | protein | 291 | 3% helix, 59% strand | C4IN73 |
| C | Fapf | protein | 284 | 4% helix, 61% strand | C4IN73 |
Ligands and binding sites
- LDA · Lauryl dimethylamine-N-oxide · additive · 5 copies · chains A, B, C
- C8E · (hydroxyethyloxy)tri(ethyloxy)octane · additive · 3 copies · chains C, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 904 | 0.78 | 0.81 | 88 | LDA |
| 2 | 830 | 0.77 | 0.81 | 74 | LDA |
| 3 | 799 | 0.77 | 0.81 | 83 | LDA |
| 4 | 316 | 0.73 | 0.86 | 39 | empty |
| 5 | 326 | 0.66 | 0.81 | 38 | LDA |
Interfaces
3 interfaces between chains.
- A–B · 895 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 865 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 819 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 5O67 · Crystal structure of the FapF polypeptide transporter - F103A mutant · 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 5O67 · PDBe 5O67 · UniProt C4IN73
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