Research workbench
Dimeric SEC14 family homolog 3 from saccharomyces cerevisiae presents some novel features of structure that lead to a surprising "dimer- monomer" state change induced by substrate binding
Analyse Dimeric SEC14 family homolog 3 from saccharomyces cerevisiae presents some… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4FMM
- Type
- protein
- Length
- 649 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phosphatidylinositol transfer protein PDR16
- UniProt
- P53860
- Ligands
- MG
- Pockets
- 7 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phosphatidylinositol transfer protein PDR16 | protein | 324 | 45% helix, 13% strand | P53860 |
| B | Phosphatidylinositol transfer protein PDR16 | protein | 325 | 45% helix, 13% strand | P53860 |
Ligands and binding sites
- MG · Magnesium ion · metal · 3 copies · chains A, B
- GOL · Glycerol · additive · 9 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1142 | 0.86 | 0.86 | 92 | GOL |
| 2 | 82 | 0.74 | 0.97 | 28 | GOL |
| 3 | 59 | 0.66 | 0.95 | 18 | GOL |
| 4 | 201 | 0.49 | 0.76 | 29 | empty |
| 5 | 51 | 0.38 | 0.81 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 1157 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 4FMM · Dimeric Sec14 family homolog 3 from Saccharomyces cerevisiae presents some novel features… · the same entry in another collection · chain A against A, TM-score 1.00
- P53860 · AlphaFold monomer V2.0 prediction for phosphatidylinositol transfer protein PDR16 (P53860) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 P53860
- Elsewhere: RCSB PDB 4FMM · PDBe 4FMM · UniProt P53860
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