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Structure of the membrane-binding domain of the SEC3 subunit of the exocyst complex
Analyse Structure of the membrane-binding domain of the SEC3 subunit of the exocyst… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3HIE
- Type
- protein
- Length
- 646 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Exocyst complex component SEC3
- UniProt
- P33332
- Ligands
- PO4
- Pockets
- 10 · best druggability 0.50
Structure
x-ray diffraction · 4 distinct chains · 25% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Exocyst complex component SEC3 | protein | 161 | 25% helix, 36% strand | P33332 |
| B | Exocyst complex component SEC3 | protein | 163 | 25% helix, 39% strand | P33332 |
| C | Exocyst complex component SEC3 | protein | 164 | 25% helix, 38% strand | P33332 |
| D | Exocyst complex component SEC3 | protein | 158 | 25% helix, 41% strand | P33332 |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 163 | 0.50 | 0.78 | 23 | empty |
| 2 | 139 | 0.45 | 0.77 | 24 | empty |
| 3 | 123 | 0.45 | 0.77 | 20 | empty |
| 4 | 139 | 0.44 | 0.75 | 26 | empty |
| 5 | 89 | 0.40 | 0.77 | 23 | empty |
Interfaces
3 interfaces between chains.
- C–D · 2184 Ų buried · 39 hydrogen bonds · protein-protein
- A–B · 2066 Ų buried · 42 hydrogen bonds · protein-protein
- B–C · 75 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 4 modified (engineered).
Compared structures
- 3HIE · Structure of the membrane-binding domain of the Sec3 subunit of the Exocyst complex · the same entry in another collection · chain D against D, TM-score 1.00
- P33332 · AlphaFold monomer V2.0 prediction for exocyst complex component SEC3 (P33332) · a predicted model of the same protein · chain A against A, TM-score 0.92
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 P33332
- Elsewhere: RCSB PDB 3HIE · PDBe 3HIE · UniProt P33332
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