MolNFT v1 · #125676 · protein
Crystal structure of the SEC3/SSO2 complex at 2.9 ångström resolution
5LG4 · Protein SSO2: “Crystal structure of the SEC3/SSO2 complex at 2.9 ångström resolution”. X-ray diffraction, 1 ligand (SO4), 8 pockets (best druggability 0.77). MolNFT v1 #125676 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 5LG4
- Type
- protein
- Length
- 534 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein SSO2; Exocyst complex component SEC3
- UniProt
- P39926, P33332
- Ligands
- SO4
- Pockets
- 8 · best druggability 0.77
Structure
x-ray diffraction · 3 distinct chains · 47% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein SSO2 | protein | 188 | 79% helix, 0% strand | P39926 |
| B | Exocyst complex component SEC3 | protein | 174 | 30% helix, 36% strand | P33332 |
| C | Exocyst complex component SEC3 | protein | 172 | 30% helix, 33% strand | P33332 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 677 | 0.77 | 0.82 | 57 | empty |
| 2 | 160 | 0.59 | 0.83 | 25 | empty |
| 3 | 134 | 0.55 | 0.82 | 23 | empty |
| 4 | 66 | 0.38 | 0.79 | 14 | empty |
| 5 | 58 | 0.36 | 0.78 | 15 | empty |
Interfaces
2 interfaces between chains.
- A–B · 738 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 603 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 5LG4 · Crystal structure of the Sec3/Sso2 complex at 2.9 angstrom resolution · the same entry in another collection · chain A against A, TM-score 1.00
- P33332 · AlphaFold monomer V2.0 prediction for exocyst complex component SEC3 (P33332) · a predicted model of the same protein · chain B against A, TM-score 0.99
- P39926 · AlphaFold monomer V2.0 prediction for protein SSO2 (P39926) · a predicted model of the same protein · chain A against A, TM-score 0.93
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 P39926
- Every structure of UniProt P33332
- Elsewhere: RCSB PDB 5LG4 · PDBe 5LG4 · UniProt P39926 · UniProt P33332
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