MolNFT v1 · #89298 · protein + DNA
Human DNA polymerase eta fails to extend primer 2 nucleotide after cisplatin crosslink (pt-GG4).
4DL7: “Human DNA polymerase eta fails to extend primer 2 nucleotide after cisplatin crosslink (pt-GG4).”. X-ray diffraction, 2 ligands (DZ4, CPT), 5 pockets (best druggability 0.79). MolNFT v1 #89298 on GenesisL1: 3D structure, binding…
- PDB
- 4DL7
- Type
- protein + DNA
- Length
- 445 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase eta; DNA (5'-D(*TP*AP*CP*TP*CP*GP*GP*TP*CP*AP*CP*T)-3'); DNA…
- EC
- 2.7.7.7
- UniProt
- Q9Y253
- Ligands
- DZ4, CPT
- Pockets
- 5 · best druggability 0.79
Structure
x-ray diffraction · 3 distinct chains · 45% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase eta (EC 2.7.7.7) | protein | 426 | 45% helix, 23% strand | Q9Y253 |
| T | DNA (5'-D(*TP*AP*CP*TP*CP*GP*GP*TP*CP*AP*CP*T)-3') | dna | 11 | — | — |
| P | DNA (5'-D(*TP*AP*GP*TP*GP*AP*CP*CP*G)-3') | dna | 8 | — | — |
Ligands and binding sites
- DZ4 · 2'-deoxy-5'-O-[(R)-hydroxy{[(r)-hydroxy(phosphonooxy) phosphoryl]amino}phosphoryl]adenosine · ligand · chains A
- CPT · Cisplatin · ligand · chains A, T
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 945 | 0.79 | 0.82 | 64 | DZ4 |
| 2 | 551 | 0.74 | 0.82 | 41 | CPT |
| 3 | 203 | 0.65 | 0.84 | 24 | empty |
| 4 | 218 | 0.61 | 0.82 | 34 | empty |
| 5 | 115 | 0.41 | 0.76 | 19 | empty |
Interfaces
3 interfaces between chains.
- A–T · 991 Ų buried · 19 hydrogen bonds · protein-nucleic
- A–P · 566 Ų buried · 9 hydrogen bonds · protein-nucleic
- T–P · 396 Ų buried · 39 hydrogen bonds · nucleic-nucleic
Compared structures
- 4DL7 · Human DNA polymerase eta fails to extend primer 2 nucleotide after cisplatin crosslink… · 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 4DL7 · PDBe 4DL7 · UniProt Q9Y253
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