MolNFT v1 · #124450 · protein + DNA
Human DNA polymerase eta-DNA ternary complex with sp-datp-alpha-S: ground state at PH7.0 (K+ mes) with 1 CA2+ ion
5KFM: “Human DNA polymerase eta-DNA ternary complex with sp-datp-alpha-S: ground state at PH7.0 (K+ mes) with 1 CA2+…”. X-ray diffraction, 2 ligands (STP, CA), 6 pockets (best druggability 0.79). MolNFT v1 #124450 on GenesisL1: 3D…
- PDB
- 5KFM
- Type
- protein + DNA
- Length
- 446 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
- STP, CA
- Pockets
- 6 · best druggability 0.79
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 | 427 | 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*T)-3') | dna | 8 | — | — |
Ligands and binding sites
- STP · 2'-deoxyadenosine 5'-O-(1-thiotriphosphate) · ligand · chains A, T, P
- CA · Calcium ion · metal · chains A
- 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 | 932 | 0.79 | 0.81 | 63 | CA, STP |
| 2 | 470 | 0.72 | 0.82 | 40 | empty |
| 3 | 226 | 0.65 | 0.83 | 23 | empty |
| 4 | 105 | 0.46 | 0.80 | 20 | empty |
| 5 | 99 | 0.37 | 0.75 | 17 | empty |
Interfaces
3 interfaces between chains.
- A–T · 1063 Ų buried · 22 hydrogen bonds · protein-nucleic
- A–P · 584 Ų buried · 13 hydrogen bonds · protein-nucleic
- T–P · 372 Ų buried · 24 hydrogen bonds · nucleic-nucleic
Compared structures
- 5KFM · Human DNA polymerase eta-DNA ternary complex with Sp-dATP-alpha-S: ground state at pH7.0… · 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 5KFM · PDBe 5KFM · UniProt Q9Y253
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