Research workbench
Structure of human DNA polymerase kappa in complex with lucidin- derived DNA adduct and incoming dampnpp
Analyse Structure of human DNA polymerase kappa in complex with lucidin- derived DNA… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5W2C
- 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*CP*GP*GP*AP*TP*CP*GP*AP*C)-3'); DNA…
- EC
- 2.7.7.7
- UniProt
- Q9UBT6
- Ligands
- DZ4, MG
- Pockets
- 10 · best druggability 0.80
Structure
x-ray diffraction · 3 distinct chains · 51% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | DNA polymerase kappa (EC 2.7.7.7) | protein | 431 | 51% helix, 19% strand | Q9UBT6 |
| C, P | DNA (5'-D(P*CP*GP*GP*AP*TP*CP*GP*AP*C)-3') | dna | 9 | — | — |
| D, T | DNA (5'-D(*CP*TP*AP*TP*(LDG)P*TP*CP*GP*AP*TP*CP*CP*G)-3') | dna | 13 | — | — |
Ligands and binding sites
- DZ4 · 2'-deoxy-5'-O-[(R)-hydroxy{[(r)-hydroxy(phosphonooxy) phosphoryl]amino}phosphoryl]adenosine · ligand · 2 copies · chains A, C, D, B, P, T
- MG · Magnesium ion · metal · 6 copies · chains A, C, B, P
- GOL · Glycerol · additive · 2 copies · chains A, D, B, T
- EDO · 1,2-ethanediol · additive · 2 copies · chains A
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 927 | 0.80 | 0.83 | 82 | empty |
| 2 | 950 | 0.80 | 0.82 | 60 | empty |
| 3 | 1027 | 0.78 | 0.80 | 63 | empty |
| 4 | 885 | 0.78 | 0.81 | 74 | MG, GOL, DZ4 |
| 5 | 821 | 0.73 | 0.78 | 52 | empty |
Interfaces
9 interfaces between chains.
- A–B · 1551 Ų buried · 36 hydrogen bonds · protein-protein
- A–D · 991 Ų buried · 20 hydrogen bonds · protein-nucleic
- B–T · 979 Ų buried · 16 hydrogen bonds · protein-nucleic
- B–P · 659 Ų buried · 18 hydrogen bonds · protein-nucleic
- A–C · 639 Ų buried · 21 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 2 modified (nucleotide modification).
Compared structures
- 5W2C · Structure of human DNA polymerase kappa in complex with Lucidin-derived DNA adduct and… · the same entry in another collection · chain C against C, 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 5W2C · PDBe 5W2C · UniProt Q9UBT6
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