Research workbench
Crystal structure of semisweet in the inward-open conformation
Analyse Crystal structure of semisweet in the inward-open conformation in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4X5M
- Type
- protein
- Length
- 272 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uncharacterized protein
- UniProt
- T8UDF6
- Ligands
- OLA, OLB, SO4
- Pockets
- 4 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 85% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Uncharacterized protein | protein | 86 | 85% helix, 0% strand | T8UDF6 |
| B | Uncharacterized protein | protein | 93 | 87% helix, 0% strand | T8UDF6 |
| C | Uncharacterized protein | protein | 93 | 84% helix, 0% strand | T8UDF6 |
Ligands and binding sites
- OLA · Oleic acid · ligand · 11 copies · chains A, B, C
- OLB · (2S)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 2 copies · chains B, C
- OLC · (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate · additive · 2 copies · chains B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 610 | 0.81 | 0.86 | 50 | OLC |
| 2 | 220 | 0.53 | 0.76 | 27 | OLA |
| 3 | 113 | 0.38 | 0.74 | 24 | OLB |
| 4 | 73 | 0.31 | 0.73 | 17 | OLA |
Interfaces
3 interfaces between chains.
- B–C · 1522 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 363 Ų buried · 1 hydrogen bond · protein-protein
- A–C · 107 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4X5M · Crystal structure of SemiSWEET in the inward-open conformation · 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 T8UDF6
- Elsewhere: RCSB PDB 4X5M · PDBe 4X5M · UniProt T8UDF6
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