MolNFT v1 · #142258 · protein + DNA
Crystal structure of human MGME1 with 3' overhang double strand DNA3
5ZYT · Mitochondrial genome maintenance exonuclease 1: “Crystal structure of human MGME1 with 3' overhang double strand DNA3”. X-ray diffraction, 20 pockets (best druggability 0.79). MolNFT v1 #142258 on GenesisL1: 3D structure, binding…
- PDB
- 5ZYT
- Type
- protein + DNA
- Length
- 923 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mitochondrial genome maintenance exonuclease 1; DNA (5'-D(P*CP*TP*TP*CP*TP*TP*CP*C)-3')
- EC
- 3.1.-.-
- UniProt
- Q9BQP7
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · 8 distinct chains · 49% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Mitochondrial genome maintenance exonuclease 1 (EC 3.1.-.-) | protein | 220 | 49% helix, 22% strand | Q9BQP7 |
| B | Mitochondrial genome maintenance exonuclease 1 (EC 3.1.-.-) | protein | 219 | 50% helix, 22% strand | Q9BQP7 |
| C | Mitochondrial genome maintenance exonuclease 1 (EC 3.1.-.-) | protein | 220 | 48% helix, 22% strand | Q9BQP7 |
| D | Mitochondrial genome maintenance exonuclease 1 (EC 3.1.-.-) | protein | 220 | 48% helix, 22% strand | Q9BQP7 |
| E | DNA (5'-D(P*CP*TP*TP*CP*TP*TP*CP*C)-3') | dna | 7 | — | — |
| F | DNA (5'-D(P*CP*TP*TP*CP*TP*TP*CP*C)-3') | dna | 11 | — | — |
| G | DNA (5'-D(P*CP*TP*TP*CP*TP*TP*CP*C)-3') | dna | 17 | — | — |
| H | DNA (5'-D(P*CP*TP*TP*CP*TP*TP*CP*C)-3') | dna | 9 | — | — |
Pockets
20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 125 | 0.79 | 0.97 | 21 | empty |
| 2 | 124 | 0.78 | 0.96 | 20 | empty |
| 3 | 139 | 0.72 | 0.91 | 26 | empty |
| 4 | 494 | 0.68 | 0.79 | 42 | empty |
| 5 | 264 | 0.65 | 0.82 | 34 | empty |
Interfaces
14 interfaces between chains.
- C–D · 2530 Ų buried · 35 hydrogen bonds · protein-protein
- A–B · 2399 Ų buried · 39 hydrogen bonds · protein-protein
- C–G · 1250 Ų buried · 17 hydrogen bonds · protein-nucleic
- D–H · 1166 Ų buried · 19 hydrogen bonds · protein-nucleic
- B–F · 1155 Ų buried · 19 hydrogen bonds · protein-nucleic
Compared structures
- 5ZYT · Crystal structure of human MGME1 with 3' overhang double strand DNA3 · the same entry in another collection · chain B against B, 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 0.89
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 5ZYT · PDBe 5ZYT · UniProt Q9BQP7
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