Research workbench
Crystal structure of human polymerase eta inserting dampnpp opposite DNA template containing an abasic site
Analyse Crystal structure of human polymerase eta inserting dampnpp opposite DNA… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4RNM
- 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 template: CAT(3DR)ATGACGCT; DNA primar: agcgtcat
- EC
- 2.7.7.7
- UniProt
- Q9Y253
- Ligands
- DZ4, MG
- Pockets
- 4 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 44% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase eta (EC 2.7.7.7) | protein | 430 | 44% helix, 22% strand | Q9Y253 |
| T | DNA template: CAT(3DR)ATGACGCT | dna | 11 | — | — |
| P | DNA primar: agcgtcat | dna | 8 | — | — |
Ligands and binding sites
- DZ4 · 2'-deoxy-5'-O-[(R)-hydroxy{[(r)-hydroxy(phosphonooxy) phosphoryl]amino}phosphoryl]adenosine · ligand · chains A, T, P
- 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
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 884 | 0.81 | 0.83 | 64 | DZ4, GOL |
| 2 | 508 | 0.73 | 0.82 | 59 | empty |
| 3 | 203 | 0.66 | 0.85 | 20 | empty |
| 4 | 94 | 0.39 | 0.76 | 17 | empty |
Interfaces
3 interfaces between chains.
- A–T · 1048 Ų buried · 17 hydrogen bonds · protein-nucleic
- A–P · 607 Ų buried · 14 hydrogen bonds · protein-nucleic
- T–P · 372 Ų buried · 34 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 4RNM · Crystal structure of human polymerase eta inserting dAMPnPP opposite DNA template… · 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 4RNM · PDBe 4RNM · UniProt Q9Y253
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