MolNFT v1 · #137884 · protein + DNA
Structure of human DNA polymerase kappa in complex with lucidin- derived DNA adduct and incoming dcmpnpp
5W2A: “Structure of human DNA polymerase kappa in complex with lucidin- derived DNA adduct and incoming dcmpnpp”. X-ray diffraction, 2 ligands (0KX, MG), 9 pockets (best druggability 0.81). MolNFT v1 #137884 on GenesisL1: 3D structure…
- PDB
- 5W2A
- 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*G)-3'); DNA…
- EC
- 2.7.7.7
- UniProt
- Q9UBT6
- Ligands
- 0KX, MG
- Pockets
- 9 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 50% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | DNA polymerase kappa (EC 2.7.7.7) | protein | 431 | 50% helix, 18% strand | Q9UBT6 |
| C, P | DNA (5'-D(P*GP*CP*GP*GP*AP*TP*CP*AP*G)-3') | dna | 9 | — | — |
| D, T | DNA (5'-D(*AP*TP*GP*(LDG)P*CP*TP*GP*AP*TP*CP*CP*GP*C)-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
- MG · Magnesium ion · metal · 2 copies · chains A, B
- GOL · Glycerol · additive · 4 copies · chains A, B, P, T
- PGE · Triethylene glycol · additive · 2 copies · chains A, D, B, T
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1165 | 0.81 | 0.83 | 97 | empty |
| 2 | 807 | 0.80 | 0.83 | 58 | empty |
| 3 | 1067 | 0.80 | 0.81 | 76 | empty |
| 4 | 908 | 0.78 | 0.81 | 73 | MG, 0KX |
| 5 | 1145 | 0.76 | 0.79 | 81 | MG, GOL, 0KX, PGE |
Interfaces
9 interfaces between chains.
- A–B · 1415 Ų buried · 32 hydrogen bonds · protein-protein
- A–D · 1107 Ų buried · 22 hydrogen bonds · protein-nucleic
- B–T · 1086 Ų buried · 18 hydrogen bonds · protein-nucleic
- B–P · 648 Ų buried · 17 hydrogen bonds · protein-nucleic
- A–C · 646 Ų buried · 17 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 2 modified (nucleotide modification).
Compared structures
- 5W2A · Structure of human DNA polymerase kappa in complex with Lucidin-derived DNA adduct and… · the same entry in another collection · chain D against D, 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 5W2A · PDBe 5W2A · UniProt Q9UBT6
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