MolNFT v1 · #107315 · protein + DNA
Structural mechanism of error-free bypass of major BENZO[A]PYRENE adduct by human polymerase kappa
4U6P · DNA polymerase kappa: “Structural mechanism of error-free bypass of major BENZO[A]PYRENE adduct by human polymerase kappa”. X-ray diffraction, 2 ligands (DCT, MG), 8 pockets (best druggability 0.80). MolNFT v1 #107315 on GenesisL1…
- PDB
- 4U6P
- Type
- protein + DNA
- Length
- 906 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase kappa; DNA (5'-D(P*GP*CP*GP*GP*AP*TP*CP*AP*C)-3'); DNA…
- EC
- 2.7.7.7
- UniProt
- Q9UBT6
- Ligands
- DCT, MG
- Pockets
- 8 · best druggability 0.80
Structure
x-ray diffraction · 3 distinct chains · 48% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | DNA polymerase kappa (EC 2.7.7.7) | protein | 431 | 48% helix, 19% strand | Q9UBT6 |
| C, P | DNA (5'-D(P*GP*CP*GP*GP*AP*TP*CP*AP*C)-3') | dna | 9 | — | — |
| D, T | DNA (5'-D(*TP*AP*TP*GP*GP*TP*GP*AP*TP*CP*CP*GP*C)-3') | dna | 13 | — | — |
Ligands and binding sites
- DCT · 2',3'-dideoxycytidine 5'-triphosphate · ligand · 2 copies · chains A, C, D, B, P, T
- MG · Magnesium ion · metal · 6 copies · chains A, C, B, P
- PGE · Triethylene glycol · additive · chains B, P, T
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1036 | 0.80 | 0.82 | 105 | MG, DCT |
| 2 | 984 | 0.78 | 0.80 | 61 | empty |
| 3 | 896 | 0.77 | 0.80 | 60 | PGE |
| 4 | 857 | 0.71 | 0.76 | 52 | empty |
| 5 | 597 | 0.69 | 0.78 | 44 | empty |
Interfaces
9 interfaces between chains.
- A–B · 1430 Ų buried · 32 hydrogen bonds · protein-protein
- A–D · 942 Ų buried · 18 hydrogen bonds · protein-nucleic
- B–T · 932 Ų buried · 20 hydrogen bonds · protein-nucleic
- B–P · 666 Ų buried · 19 hydrogen bonds · protein-nucleic
- A–C · 634 Ų buried · 16 hydrogen bonds · protein-nucleic
Compared structures
- 4U6P · Structural mechanism of error-free bypass of major benzo[a]pyrene adduct by human… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9UBT6 · AlphaFold monomer V2.0 prediction for DNA polymerase kappa (Q9UBT6) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 Q9UBT6
- Elsewhere: RCSB PDB 4U6P · PDBe 4U6P · UniProt Q9UBT6
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