MolNFT v1 · #144387 · protein + DNA
Crystal structure of human DNA polymerase kappa in complex with DNA containing the major cisplatin lesion
6BRX: “Crystal structure of human DNA polymerase kappa in complex with DNA containing the major cisplatin lesion”. X-ray diffraction, 3 ligands (0KX, CPT, MG), 11 pockets (best druggability 0.79). MolNFT v1 #144387 on GenesisL1: 3D…
- 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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