MolNFT v1 · #142259 · protein + DNA
The crystal structure of HUMANMGME1 with single strand DNA2
5ZYU · DNA (5'-D(P*CP*AP*AP*CP*AP*AP*CP*A)-3'): “The crystal structure of HUMANMGME1 with single strand DNA2”. X-ray diffraction, 7 pockets (best druggability 0.79). MolNFT v1 #142259 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 5ZYU
- Type
- protein + DNA
- Length
- 460 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (5'-D(P*CP*AP*AP*CP*AP*AP*CP*A)-3'); Mitochondrial genome maintenance exonuclease 1
- EC
- 3.1.-.-
- UniProt
- Q9BQP7
- Pockets
- 7 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 48% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| E, C | DNA (5'-D(P*CP*AP*AP*CP*AP*AP*CP*A)-3') | dna | 7 | — | — |
| A, B | Mitochondrial genome maintenance exonuclease 1 (EC 3.1.-.-) | protein | 223 | 48% helix, 22% strand | Q9BQP7 |
Ligands and binding sites
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 145 | 0.79 | 0.96 | 23 | empty |
| 2 | 142 | 0.78 | 0.96 | 20 | empty |
| 3 | 303 | 0.56 | 0.76 | 33 | empty |
| 4 | 241 | 0.53 | 0.76 | 28 | empty |
| 5 | 126 | 0.47 | 0.78 | 24 | empty |
Interfaces
6 interfaces between chains.
- A–B · 2499 Ų buried · 52 hydrogen bonds · protein-protein
- C–B · 1006 Ų buried · 21 hydrogen bonds · protein-nucleic
- E–A · 1005 Ų buried · 19 hydrogen bonds · protein-nucleic
- E–B · 174 Ų buried · 2 hydrogen bonds · protein-nucleic
- C–A · 167 Ų buried · 3 hydrogen bonds · protein-nucleic
Compared structures
- 5ZYU · The crystal structure of humanMGME1 with single strand DNA2 · the same entry in another collection · chain E against E, 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 0.90
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 5ZYU · PDBe 5ZYU · UniProt Q9BQP7
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