Research workbench
1.8 ångström crystal structure of succinate-acetate permease from citrobacter koseri
Analyse 1.8 ångström crystal structure of succinate-acetate permease from citrobacter… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5YS3
- Type
- protein
- Length
- 552 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Succinate-acetate permease
- UniProt
- A8ALU5
- Ligands
- PLM, 78M
- Pockets
- 8 · best druggability 0.59
Structure
x-ray diffraction · 2 distinct chains · 75% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Succinate-acetate permease | protein | 188 | 72% helix, 0% strand | A8ALU5 |
| B, C | Succinate-acetate permease | protein | 182 | 77% helix, 0% strand | A8ALU5 |
Ligands and binding sites
- PLM · Palmitic acid · ligand · 10 copies · chains A, B, C
- 78M · (2S)-2,3-dihydroxypropyl(7z)-pentadec-7-enoate · ligand · 7 copies · chains A, B, C
- ACT · Acetate ion · additive · 18 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 167 | 0.59 | 0.82 | 28 | ACT |
| 2 | 188 | 0.58 | 0.81 | 33 | ACT |
| 3 | 135 | 0.57 | 0.82 | 25 | ACT |
| 4 | 177 | 0.56 | 0.80 | 28 | ACT |
| 5 | 109 | 0.53 | 0.82 | 19 | ACT |
Interfaces
2 interfaces between chains.
- B–C · 1823 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 1774 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 5YS3 · 1.8 angstrom crystal structure of Succinate-Acetate Permease from Citrobacter koseri · the same entry in another collection · chain B against B, 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 A8ALU5
- Elsewhere: RCSB PDB 5YS3 · PDBe 5YS3 · UniProt A8ALU5
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