MolNFT v1 · #78778 · protein
Crystal structure of S. cerevisiae GET3 with bound ADP-MG2+ in complex with GET2 cytosolic domain
3SJD · ATPase GET3: “Crystal structure of S. cerevisiae GET3 with bound ADP-MG2+ in complex with GET2 cytosolic domain”. X-ray diffraction, 3 ligands (ADP, MG, ZN), 20 pockets (best druggability 0.89). MolNFT v1 #78778 on GenesisL1: 3D…
- PDB
- 3SJD
- Type
- protein
- Length
- 919 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ATPase GET3; Golgi to er traffic protein 2
- EC
- 3.6.-.-
- UniProt
- Q12154, P40056
- Ligands
- ADP, MG, ZN
- Pockets
- 20 · best druggability 0.89
Structure
x-ray diffraction · 4 distinct chains · 46% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ATPase GET3 (EC 3.6.-.-) | protein | 287 | 46% helix, 11% strand | Q12154 |
| B | ATPase GET3 (EC 3.6.-.-) | protein | 280 | 46% helix, 11% strand | Q12154 |
| C | ATPase GET3 (EC 3.6.-.-) | protein | 292 | 43% helix, 11% strand | Q12154 |
| D, E | Golgi to er traffic protein 2 | protein | 30 | 90% helix, 0% strand | P40056 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 3 copies · chains A, B, C
- MG · Magnesium ion · metal · 3 copies · chains A, B, C
- ZN · Zinc ion · metal · 2 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1021 | 0.89 | 0.91 | 104 | ADP, MG, ZN |
| 2 | 353 | 0.72 | 0.83 | 50 | empty |
| 3 | 158 | 0.71 | 0.89 | 27 | empty |
| 4 | 282 | 0.56 | 0.77 | 37 | empty |
| 5 | 188 | 0.56 | 0.80 | 26 | empty |
Interfaces
4 interfaces between chains.
- A–B · 1403 Ų buried · 8 hydrogen bonds · protein-protein
- C–D · 720 Ų buried · 13 hydrogen bonds · protein-protein
- A–E · 709 Ų buried · 13 hydrogen bonds · protein-protein
- B–D · 248 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 3 covalent (disulfide, covalent ligand).
Compared structures
- 3SJD · Crystal structure of S. cerevisiae Get3 with bound ADP-Mg2+ in complex with Get2… · the same entry in another collection · chain E against E, TM-score 1.00
- Q12154 · AlphaFold monomer V2.0 prediction for ATPase GET3 (Q12154) · a predicted model of the same protein · chain B against A, TM-score 0.89
- P40056 · AlphaFold monomer V2.0 prediction for golgi to er traffic protein 2 (P40056) · a predicted model of the same protein · chain D against A, TM-score 0.57
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 Q12154
- Every structure of UniProt P40056
- Elsewhere: RCSB PDB 3SJD · PDBe 3SJD · UniProt Q12154 · UniProt P40056
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