Research workbench
Human DNA polymerase eta extending primer immediately after cisplatin crosslink (pt-GG3).
Analyse Human DNA polymerase eta extending primer immediately after cisplatin crosslink… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4DL6
- Type
- protein + DNA
- Length
- 443 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase eta; DNA (5'-D(*TP*AP*TP*CP*GP*GP*CP*AP*CP*AP*CP*T)-3'); DNA…
- EC
- 2.7.7.7
- UniProt
- Q9Y253
- Ligands
- XG4, CPT, MG
- Pockets
- 5 · best druggability 0.80
Structure
x-ray diffraction · 3 distinct chains · 46% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase eta (EC 2.7.7.7) | protein | 424 | 46% helix, 23% strand | Q9Y253 |
| T | DNA (5'-D(*TP*AP*TP*CP*GP*GP*CP*AP*CP*AP*CP*T)-3') | dna | 11 | — | — |
| P | DNA (5'-D(*TP*AP*GP*TP*GP*TP*GP*CP*C)-3') | dna | 8 | — | — |
Ligands and binding sites
- XG4 · 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]guanosine · ligand · chains A, T, P
- CPT · Cisplatin · ligand · chains T
- MG · Magnesium ion · metal · 2 copies · chains A, P
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1052 | 0.80 | 0.82 | 65 | MG, XG4 |
| 2 | 620 | 0.75 | 0.82 | 43 | CPT |
| 3 | 262 | 0.67 | 0.83 | 26 | empty |
| 4 | 106 | 0.45 | 0.79 | 19 | empty |
| 5 | 94 | 0.37 | 0.76 | 16 | empty |
Interfaces
3 interfaces between chains.
- A–T · 963 Ų buried · 22 hydrogen bonds · protein-nucleic
- A–P · 627 Ų buried · 13 hydrogen bonds · protein-nucleic
- T–P · 380 Ų buried · 32 hydrogen bonds · nucleic-nucleic
Compared structures
- 4DL6 · Human DNA polymerase eta extending primer immediately after cisplatin crosslink (Pt-GG3). · 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 4DL6 · PDBe 4DL6 · UniProt Q9Y253
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