MolNFT v1 · #144390 · protein + DNA
Crystal structure of human DNA polymerase kappa in complex with DNA containing the major cisplatin lesion
6BS1: “Crystal structure of human DNA polymerase kappa in complex with DNA containing the major cisplatin lesion”. X-ray diffraction, 4 ligands (DZ4, CPT, MG), 15 pockets (best druggability 0.75). MolNFT v1 #144390 on GenesisL1: 3D…
- PDB
- 6BS1
- 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*AP*TP*AP*CP*AP*TP*AP*CP*C)-3'); DNA…
- EC
- 2.7.7.7
- UniProt
- Q9UBT6
- Ligands
- DZ4, CPT, MG, IOD
- Pockets
- 15 · best druggability 0.75
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 | 432 | 50% helix, 19% strand | Q9UBT6 |
| B | DNA polymerase kappa (EC 2.7.7.7) | protein | 430 | 48% helix, 18% strand | Q9UBT6 |
| C, P | DNA (5'-D(P*AP*TP*AP*CP*AP*TP*AP*CP*C)-3') | dna | 9 | — | — |
| D, T | DNA (5'-D(*TP*AP*CP*TP*GP*GP*TP*AP*TP*GP*TP*AP*T)-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
- CPT · Cisplatin · ligand · 2 copies · chains C, D, P, T
- MG · Magnesium ion · metal · 6 copies · chains A, C, B, P
- IOD · Iodide ion · ion · 9 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 969 | 0.75 | 0.78 | 63 | IOD, CPT |
| 2 | 576 | 0.75 | 0.82 | 45 | CPT |
| 3 | 645 | 0.71 | 0.79 | 48 | empty |
| 4 | 287 | 0.68 | 0.83 | 40 | empty |
| 5 | 350 | 0.67 | 0.82 | 41 | empty |
Interfaces
9 interfaces between chains.
- A–B · 1480 Ų buried · 35 hydrogen bonds · protein-protein
- A–D · 1006 Ų buried · 23 hydrogen bonds · protein-nucleic
- B–T · 972 Ų buried · 21 hydrogen bonds · protein-nucleic
- A–C · 659 Ų buried · 21 hydrogen bonds · protein-nucleic
- B–P · 637 Ų buried · 21 hydrogen bonds · protein-nucleic
Compared structures
- 6BS1 · 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 6BS1 · PDBe 6BS1 · UniProt Q9UBT6
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