MolNFT v1 · #124466 · protein + DNA
Human DNA polymerase eta-DNA ternary complex: reaction first with 1 mm MN2+ for 1800S then with 5 mm MN2+ for 60S at 37 degree
5KG2: “Human DNA polymerase eta-DNA ternary complex: reaction first with 1 mm MN2+ for 1800S then with 5 mm MN2+ for…”. X-ray diffraction, 3 ligands (DTP, DPO, MN), 6 pockets (best druggability 0.74). MolNFT v1 #124466 on GenesisL1: 3D…
- PDB
- 5KG2
- Type
- protein + DNA
- Length
- 450 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
- Ligands
- DTP, DPO, MN
- Pockets
- 6 · best druggability 0.74
Structure
x-ray diffraction · 3 distinct chains · 43% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase eta (EC 2.7.7.7) | protein | 430 | 43% helix, 22% 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
- DTP · 2'-deoxyadenosine 5'-triphosphate · ligand · chains A, T, P
- DPO · Diphosphate · ligand · chains A, P
- MN · Manganese (II) ion · metal · 3 copies · chains A, P
- GOL · Glycerol · additive · 3 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 532 | 0.74 | 0.83 | 37 | empty |
| 2 | 536 | 0.70 | 0.80 | 50 | empty |
| 3 | 225 | 0.66 | 0.84 | 24 | empty |
| 4 | 237 | 0.49 | 0.75 | 28 | DPO, MN |
| 5 | 102 | 0.47 | 0.80 | 20 | empty |
Interfaces
3 interfaces between chains.
- A–T · 1018 Ų buried · 21 hydrogen bonds · protein-nucleic
- A–P · 796 Ų buried · 20 hydrogen bonds · protein-nucleic
- T–P · 425 Ų buried · 33 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 5KG2 · Human DNA polymerase eta-DNA ternary complex: reaction first with 1 mM Mn2+ for 1800s… · 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 5KG2 · PDBe 5KG2 · UniProt Q9Y253
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