Research workbench
Crystal structure of SEC3P - RHO1P complex from saccharomyces cerevisiae
Analyse Crystal structure of SEC3P - RHO1P complex from saccharomyces cerevisiae in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3A58
- Type
- protein
- Length
- 1,068 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Exocyst complex component SEC3; GTP-binding protein RHO1
- UniProt
- P33332, P06780
- Ligands
- GNP, MG, PO4
- Pockets
- 11 · best druggability 0.72
Structure
x-ray diffraction · 5 distinct chains · 35% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Exocyst complex component SEC3 | protein | 185 | 30% helix, 31% strand | P33332 |
| B, D | GTP-binding protein RHO1 | protein | 178 | 40% helix, 24% strand | P06780 |
| C | Exocyst complex component SEC3 | protein | 180 | 31% helix, 32% strand | P33332 |
| E | Exocyst complex component SEC3 | protein | 166 | 34% helix, 34% strand | P33332 |
| F | GTP-binding protein RHO1 | protein | 181 | 40% helix, 24% strand | P06780 |
Ligands and binding sites
- GNP · Phosphoaminophosphonic acid-guanylate ester · ligand · 3 copies · chains B, D, F
- MG · Magnesium ion · metal · 3 copies · chains B, D, F
- PO4 · Phosphate ion · ion · 7 copies · chains A, C, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 592 | 0.72 | 0.80 | 73 | GNP, MG |
| 2 | 485 | 0.69 | 0.80 | 64 | PO4, GNP, MG |
| 3 | 449 | 0.69 | 0.80 | 54 | GNP, MG |
| 4 | 232 | 0.53 | 0.77 | 37 | empty |
| 5 | 68 | 0.43 | 0.81 | 17 | empty |
Interfaces
5 interfaces between chains.
- E–F · 785 Ų buried · 4 hydrogen bonds · protein-protein
- C–D · 781 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 749 Ų buried · 7 hydrogen bonds · protein-protein
- C–F · 230 Ų buried · 5 hydrogen bonds · protein-protein
- B–F · 36 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 3 modified (engineered).
Compared structures
- 3A58 · Crystal structure of Sec3p - Rho1p complex from Saccharomyces cerevisiae · the same entry in another collection · chain F against F, TM-score 1.00
- P33332 · AlphaFold monomer V2.0 prediction for exocyst complex component SEC3 (P33332) · a predicted model of the same protein · chain E against A, TM-score 0.99
- P06780 · AlphaFold monomer V2.0 prediction for GTP-binding protein RHO1 (P06780) · a predicted model of the same protein · chain B against A, TM-score 0.98
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
- Every structure of UniProt P06780
- Elsewhere: RCSB PDB 3A58 · PDBe 3A58 · UniProt P33332 · UniProt P06780
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