MolNFT v1 · #124446 · protein + DNA
Human DNA polymerase eta-DNA ternary complex: reaction with 10 mm MN2+ for 120S
5KFI: “Human DNA polymerase eta-DNA ternary complex: reaction with 10 mm MN2+ for 120S”. X-ray diffraction, 4 ligands (DTP, DPO, MN), 6 pockets (best druggability 0.75). MolNFT v1 #124446 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5KFI
- 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, CA
- Pockets
- 6 · best druggability 0.75
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
- CA · Calcium ion · metal · 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 567 | 0.75 | 0.83 | 38 | empty |
| 2 | 536 | 0.73 | 0.82 | 49 | empty |
| 3 | 224 | 0.65 | 0.84 | 23 | empty |
| 4 | 248 | 0.52 | 0.76 | 32 | CA, MN, DPO |
| 5 | 102 | 0.47 | 0.80 | 20 | empty |
Interfaces
3 interfaces between chains.
- A–T · 1047 Ų buried · 22 hydrogen bonds · protein-nucleic
- A–P · 781 Ų buried · 20 hydrogen bonds · protein-nucleic
- T–P · 427 Ų buried · 30 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 5KFI · Human DNA polymerase eta-DNA ternary complex: reaction with 10 mM Mn2+ for 120s · 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 5KFI · PDBe 5KFI · UniProt Q9Y253
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