Research workbench
Crystal structure of human DNA polymerase kappa in complex with DNA containing the major cisplatin lesion
Analyse Crystal structure of human DNA polymerase kappa in complex with DNA containing… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6BRX
- Type
- protein + DNA
- Length
- 907 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase kappa; DNA (5'-D(P*TP*AP*CP*AP*TP*AP*CP*AP*C)-3'); DNA…
- EC
- 2.7.7.7
- UniProt
- Q9UBT6
- Ligands
- 0KX, CPT, MG
- Pockets
- 11 · best druggability 0.79
Structure
x-ray diffraction · 4 distinct chains · 49% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase kappa (EC 2.7.7.7) | protein | 433 | 49% helix, 19% strand | Q9UBT6 |
| B | DNA polymerase kappa (EC 2.7.7.7) | protein | 430 | 50% helix, 19% strand | Q9UBT6 |
| C, P | DNA (5'-D(P*TP*AP*CP*AP*TP*AP*CP*AP*C)-3') | dna | 9 | — | — |
| D, T | DNA (5'-D(*TP*AP*TP*GP*GP*TP*GP*TP*AP*TP*GP*TP*A)-3') | dna | 13 | — | — |
Ligands and binding sites
- 0KX · 2'-deoxy-5'-O-[(R)-hydroxy{[(r)-hydroxy(phosphonooxy) phosphoryl]amino}phosphoryl]cytidine · ligand · 2 copies · chains A, C, D, B, P, T
- CPT · Cisplatin · ligand · 2 copies · chains D, T
- MG · Magnesium ion · metal · 5 copies · chains A, C, B, P
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains A, C, D, P, T
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 750 | 0.79 | 0.83 | 74 | empty |
| 2 | 1006 | 0.78 | 0.80 | 60 | CPT |
| 3 | 827 | 0.75 | 0.80 | 51 | CPT |
| 4 | 885 | 0.72 | 0.77 | 51 | empty |
| 5 | 829 | 0.71 | 0.77 | 49 | empty |
Interfaces
9 interfaces between chains.
- A–B · 1451 Ų buried · 40 hydrogen bonds · protein-protein
- A–D · 979 Ų buried · 26 hydrogen bonds · protein-nucleic
- B–T · 963 Ų buried · 21 hydrogen bonds · protein-nucleic
- B–P · 670 Ų buried · 22 hydrogen bonds · protein-nucleic
- A–C · 641 Ų buried · 21 hydrogen bonds · protein-nucleic
Compared structures
- 6BRX · Crystal Structure of Human DNA polymerase kappa in complex with DNA containing the major… · the same entry in another collection · chain T against T, TM-score 1.00
- Q9UBT6 · AlphaFold monomer V2.0 prediction for DNA polymerase kappa (Q9UBT6) · a predicted model of the same protein · chain B 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 6BRX · PDBe 6BRX · UniProt Q9UBT6
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