MolNFT v2 · #157593 · protein + DNA
Human DNA polymerase eta extension complex with cdA at the -2 position
6M7P: “Human DNA polymerase eta extension complex with cdA at the -2 position”. X-ray diffraction at 1.75, 2 ligands (DZ4, MG), 5 pockets (best druggability 0.80). MolNFT v2 #157593 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 6M7P
- Type
- protein + DNA
- Length
- 447 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.75
- Source
- Homo sapiens; SYNTHETIC CONSTRUCT
- Molecule
- DNA polymerase eta; DNA (5'-D(*CP*AP*TP*TP*CP*(02I)P*CP*AP*CP*AP*CP*T)-3'); DNA…
- EC
- 2.7.7.7
- UniProt
- Q9Y253
- Ligands
- DZ4, MG
- Pockets
- 5 · best druggability 0.80
Structure
x-ray diffraction · resolution 1.75 · 3 distinct chains · 44% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase eta (EC 2.7.7.7) | protein | 428 | 44% helix, 22% strand | Q9Y253 |
| T | DNA (5'-D(*CP*AP*TP*TP*CP*(02I)P*CP*AP*CP*AP*CP*T)-3') | dna | 11 | — | — |
| P | DNA (5'-D(*AP*GP*TP*GP*TP*GP*TP*G)-3') | dna | 8 | — | — |
Ligands and binding sites
- DZ4 · 2'-deoxy-5'-O-[(R)-hydroxy{[(r)-hydroxy(phosphonooxy) phosphoryl]amino}phosphoryl]adenosine · ligand · chains A, T, P
- MG · Magnesium ion · metal · 2 copies · chains A, P
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 989 | 0.80 | 0.81 | 65 | DZ4, MG |
| 2 | 587 | 0.74 | 0.82 | 53 | empty |
| 3 | 200 | 0.68 | 0.86 | 21 | empty |
| 4 | 89 | 0.49 | 0.83 | 22 | empty |
| 5 | 90 | 0.37 | 0.76 | 16 | empty |
Interfaces
3 interfaces between chains.
- A–T · 985 Ų buried · 20 hydrogen bonds · protein-nucleic
- A–P · 587 Ų buried · 12 hydrogen bonds · protein-nucleic
- T–P · 379 Ų buried · 27 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 6M7P · Human DNA polymerase eta extension complex with cda at the -2 position · the same entry in another collection · 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 Q9Y253
- Elsewhere: RCSB PDB 6M7P · PDBe 6M7P · UniProt Q9Y253
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