Research workbench
Crystal structure of human MGME1 with single strand DNA2 and CA2+
Analyse Crystal structure of human MGME1 with single strand DNA2 and CA2+ in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5ZYV
- Type
- protein + DNA
- Length
- 203 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mitochondrial genome maintenance exonuclease 1; DNA (5'-D(P*CP*AP*AP*CP*AP*AP*T)-3')
- EC
- 3.1.-.-
- UniProt
- Q9BQP7
- Ligands
- CA
- Pockets
- 3 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 52% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Mitochondrial genome maintenance exonuclease 1 (EC 3.1.-.-) | protein | 197 | 52% helix, 23% strand | Q9BQP7 |
| E | DNA (5'-D(P*CP*AP*AP*CP*AP*AP*T)-3') | dna | 6 | — | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 91 | 0.74 | 0.96 | 19 | empty |
| 2 | 88 | 0.36 | 0.75 | 16 | empty |
| 3 | 75 | 0.32 | 0.74 | 14 | empty |
Interfaces
1 interface between chains.
- A–E · 977 Ų buried · 17 hydrogen bonds · protein-nucleic
Compared structures
- 5ZYV · Crystal structure of human MGME1 with single strand DNA2 and Ca2+ · the same entry in another collection · chain A against A, TM-score 1.00
- Q9BQP7 · AlphaFold monomer V2.0 prediction for mitochondrial genome maintenance exonuclease 1… · a predicted model of the same protein · chain A against A, TM-score 0.97
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 Q9BQP7
- Elsewhere: RCSB PDB 5ZYV · PDBe 5ZYV · UniProt Q9BQP7
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