Research workbench
Crystal structure of GET3 from methanocaldococcus jannaschii
Analyse Crystal structure of GET3 from methanocaldococcus jannaschii in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3UG6
- Type
- protein
- Length
- 1,212 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Arsenical pump-driving ATPase
- EC
- 3.6.3.16
- UniProt
- Q58542
- Ligands
- ADP, MG, ZN
- Pockets
- 15 · best druggability 0.90
Structure
x-ray diffraction · 1 distinct chain · 57% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Arsenical pump-driving ATPase (EC 3.6.3.16) | protein | 303 | 57% helix, 15% strand | Q58542 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
- ZN · Zinc ion · metal · 2 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 954 | 0.90 | 0.92 | 123 | ADP, MG |
| 2 | 500 | 0.87 | 0.93 | 63 | ADP |
| 3 | 375 | 0.80 | 0.90 | 55 | empty |
| 4 | 998 | 0.74 | 0.77 | 78 | empty |
| 5 | 975 | 0.74 | 0.77 | 80 | empty |
Interfaces
6 interfaces between chains.
- C–D · 3195 Ų buried · 42 hydrogen bonds · protein-protein
- A–B · 3156 Ų buried · 38 hydrogen bonds · protein-protein
- B–C · 1800 Ų buried · 13 hydrogen bonds · protein-protein
- A–D · 1760 Ų buried · 10 hydrogen bonds · protein-protein
- B–D · 270 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 3UG6 · Crystal Structure of Get3 from Methanocaldococcus jannaschii · the same entry in another collection · chain D against D, TM-score 1.00
- Q58542 · AlphaFold monomer V2.0 prediction for putative arsenical pump-driving ATPase (Q58542) · a predicted model of the same protein · chain C against A, TM-score 0.94
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 Q58542
- Elsewhere: RCSB PDB 3UG6 · PDBe 3UG6 · UniProt Q58542
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