Research workbench
Polymerase eta-catalyzed insertion of the mismatched a opposite template cytarabine (arac) residue
Analyse Polymerase eta-catalyzed insertion of the mismatched a opposite template… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6Q02
- Type
- protein + DNA
- Length
- 449 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase eta; DNA primer strand; DNA template containing a cytarabin (arac) residue
- EC
- 2.7.7.7
- UniProt
- Q9Y253
- Ligands
- DZ4, MG
- Pockets
- 6 · best druggability 0.80
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 |
| P | DNA primer strand | dna | 8 | — | — |
| T | DNA template containing a cytarabin (arac) residue | dna | 11 | — | — |
Ligands and binding sites
- DZ4 · 2'-deoxy-5'-O-[(R)-hydroxy{[(r)-hydroxy(phosphonooxy) phosphoryl]amino}phosphoryl]adenosine · ligand · chains A, P, T
- MG · Magnesium ion · metal · 2 copies · chains A, P
- 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1010 | 0.80 | 0.82 | 72 | MG, DZ4 |
| 2 | 585 | 0.75 | 0.82 | 47 | empty |
| 3 | 237 | 0.67 | 0.84 | 25 | empty |
| 4 | 92 | 0.46 | 0.81 | 23 | empty |
| 5 | 62 | 0.42 | 0.81 | 15 | empty |
Interfaces
3 interfaces between chains.
- A–T · 957 Ų buried · 19 hydrogen bonds · protein-nucleic
- A–P · 582 Ų buried · 14 hydrogen bonds · protein-nucleic
- P–T · 378 Ų buried · 32 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 6Q02 · Polymerase Eta-catalyzed insertion of the mismatched A opposite template cytarabine… · 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 6Q02 · PDBe 6Q02 · UniProt Q9Y253
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