MolNFT v1 · #90229 · protein + DNA
Human DNA polymerase eta - DNA ternary complex: reaction in the at crystal at pH 6.7 for 15 hr, sideway translocation
4ED6: “Human DNA polymerase eta - DNA ternary complex: reaction in the at crystal at pH 6.7 for 15 hr, sideway…”. X-ray diffraction, 6 pockets (best druggability 0.75). MolNFT v1 #90229 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 4ED6
- Type
- protein + DNA
- Length
- 452 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase eta; DNA (5'-D(*CP*AP*TP*TP*AP*TP*GP*AP*CP*GP*CP*T)-3'); DNA…
- EC
- 2.7.7.7
- UniProt
- Q9Y253
- Pockets
- 6 · best druggability 0.75
Structure
x-ray diffraction · 3 distinct chains · 44% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase eta (EC 2.7.7.7) | protein | 432 | 44% helix, 21% strand | Q9Y253 |
| T | DNA (5'-D(*CP*AP*TP*TP*AP*TP*GP*AP*CP*GP*CP*T)-3') | dna | 11 | — | — |
| P | DNA (5'-D(*AP*GP*CP*GP*TP*CP*AP*TP*A)-3') | dna | 9 | — | — |
Ligands and binding sites
- GOL · Glycerol · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 548 | 0.75 | 0.83 | 37 | empty |
| 2 | 675 | 0.72 | 0.79 | 51 | empty |
| 3 | 215 | 0.66 | 0.84 | 21 | empty |
| 4 | 142 | 0.57 | 0.83 | 27 | empty |
| 5 | 229 | 0.49 | 0.75 | 32 | empty |
Interfaces
3 interfaces between chains.
- A–T · 1098 Ų buried · 21 hydrogen bonds · protein-nucleic
- A–P · 855 Ų buried · 15 hydrogen bonds · protein-nucleic
- T–P · 458 Ų buried · 33 hydrogen bonds · nucleic-nucleic
Compared structures
- 4ED6 · Human DNA polymerase eta - DNA ternary complex: Reaction in the AT crystal at pH 6.7 for… · the same entry in another collection · chain T against T, 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 4ED6 · PDBe 4ED6 · UniProt Q9Y253
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