MolNFT v1 · #119956 · protein + DNA
Crystal structure of the endog worm homologue cps-6 H148A/F122A in complex with DNA
5GKP · Endonuclease G, mitochondrial: “Crystal structure of the endog worm homologue cps-6 H148A/F122A in complex with DNA”. X-ray diffraction, 1 ligand (MG), 6 pockets (best druggability 0.73). MolNFT v1 #119956 on GenesisL1: 3D…
- PDB
- 5GKP
- Type
- protein + DNA
- Length
- 484 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Endonuclease G, mitochondrial; DNA (5'-D(*TP*TP*TP*TP*T)-3')
- EC
- 3.1.30.-
- UniProt
- Q95NM6
- Ligands
- MG
- Pockets
- 6 · best druggability 0.73
Structure
x-ray diffraction · 3 distinct chains · 25% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Endonuclease G, mitochondrial (EC 3.1.30.-) | protein | 235 | 24% helix, 31% strand | Q95NM6 |
| B | Endonuclease G, mitochondrial (EC 3.1.30.-) | protein | 239 | 26% helix, 33% strand | Q95NM6 |
| C, D | DNA (5'-D(*TP*TP*TP*TP*T)-3') | dna | 5 | — | — |
Ligands and binding sites
- MG · Magnesium ion · metal · 2 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 266 | 0.73 | 0.87 | 55 | empty |
| 2 | 70 | 0.46 | 0.83 | 13 | empty |
| 3 | 73 | 0.45 | 0.82 | 17 | empty |
| 4 | 97 | 0.44 | 0.79 | 11 | empty |
| 5 | 85 | 0.32 | 0.73 | 18 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1539 Ų buried · 25 hydrogen bonds · protein-protein
- A–C · 590 Ų buried · 13 hydrogen bonds · protein-nucleic
- B–D · 523 Ų buried · 13 hydrogen bonds · protein-nucleic
Compared structures
- 5GKP · Crystal structure of the EndoG worm homologue CPS-6 H148A/F122A in complex with DNA · the same entry in another collection · chain A against A, TM-score 1.00
- Q95NM6 · AlphaFold monomer V2.0 prediction for endonuclease G, mitochondrial (Q95NM6) · a predicted model of the same protein · chain A against A, TM-score 1.00
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 Q95NM6
- Elsewhere: RCSB PDB 5GKP · PDBe 5GKP · UniProt Q95NM6
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