MolNFT v1 · #106054 · protein + DNA
Crystal structure of human polymerase eta extending an abasic site-da pair by inserting dctp opposite template G
4RNO · DNA polymerase eta: “Crystal structure of human polymerase eta extending an abasic site-da pair by inserting dctp opposite…”. X-ray diffraction, 2 ligands (DCP, CA), 3 pockets (best druggability 0.86). MolNFT v1 #106054 on…
- PDB
- 4RNO
- Type
- protein + DNA
- Length
- 444 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase eta; Nucleic acids template: CATG(3DR)TGACGCT; Nucleic acids primar…
- EC
- 2.7.7.7
- UniProt
- Q9Y253
- Ligands
- DCP, CA
- Pockets
- 3 · best druggability 0.86
Structure
x-ray diffraction · 3 distinct chains · 42% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase eta (EC 2.7.7.7) | protein | 425 | 42% helix, 20% strand | Q9Y253 |
| T | Nucleic acids template: CATG(3DR)TGACGCT | dna | 11 | — | — |
| P | Nucleic acids primar: agcgtcaa | dna | 8 | — | — |
Ligands and binding sites
- DCP · 2'-deoxycytidine-5'-triphosphate · ligand · chains A, T, P
- CA · Calcium ion · metal · chains A
- GOL · Glycerol · additive
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1032 | 0.86 | 0.87 | 93 | DCP, CA |
| 2 | 82 | 0.41 | 0.79 | 19 | empty |
| 3 | 79 | 0.38 | 0.77 | 15 | empty |
Interfaces
3 interfaces between chains.
- A–T · 1059 Ų buried · 28 hydrogen bonds · protein-nucleic
- A–P · 563 Ų buried · 17 hydrogen bonds · protein-nucleic
- T–P · 373 Ų buried · 30 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 1 covalent, 1 modified (covalent ligand, nucleotide modification).
Compared structures
- 4RNO · Crystal structure of human polymerase eta extending an abasic site-dA pair by inserting… · 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 4RNO · PDBe 4RNO · UniProt Q9Y253
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