MolNFT v1 · #67532 · protein + DNA
Structure of human DNA polymerase kappa inserting datp opposite an 8-oxog DNA lesion
3IN5: “Structure of human DNA polymerase kappa inserting datp opposite an 8-oxog DNA lesion”. X-ray diffraction, 2 ligands (ATP, MG), 12 pockets (best druggability 0.79). MolNFT v1 #67532 on GenesisL1: 3D structure, binding sites and…
- PDB
- 3IN5
- Type
- protein + DNA
- Length
- 927 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase kappa; DNA (5'- D(*GP*G*GP*GP*GP*AP*AP*GP*GP*AP*CP*TP*(DOC))-3'); DNA…
- EC
- 2.7.7.7
- UniProt
- Q9UBT6
- Ligands
- ATP, MG
- Pockets
- 12 · best druggability 0.79
Structure
x-ray diffraction · 6 distinct chains · 50% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase kappa (EC 2.7.7.7) | protein | 438 | 50% helix, 17% strand | Q9UBT6 |
| B | DNA polymerase kappa (EC 2.7.7.7) | protein | 437 | 49% helix, 19% strand | Q9UBT6 |
| P | DNA (5'- D(*GP*G*GP*GP*GP*AP*AP*GP*GP*AP*CP*TP*(DOC))-3') | dna | 11 | — | — |
| T | DNA (5'-D(*C*CP*TP*AP*(8OG) P*GP*AP*GP*TP*CP*CP*TP*TP*CP*CP*CP*CP*C)-3') | dna | 15 | — | — |
| Q | DNA (5'- D(*GP*G*GP*GP*GP*AP*AP*GP*GP*AP*CP*TP*(DOC))-3') | dna | 12 | — | — |
| U | DNA (5'-D(*C*CP*TP*AP*(8OG) P*GP*AP*GP*TP*CP*CP*TP*TP*CP*CP*CP*CP*C)-3') | dna | 14 | — | — |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 2 copies · chains A, P, T, B, Q, U
- MG · Magnesium ion · metal · 4 copies · chains A, P, B, Q
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1010 | 0.79 | 0.81 | 81 | ATP |
| 2 | 538 | 0.79 | 0.86 | 48 | empty |
| 3 | 365 | 0.78 | 0.88 | 41 | ATP, MG |
| 4 | 737 | 0.78 | 0.83 | 49 | empty |
| 5 | 70 | 0.73 | 0.98 | 23 | empty |
Interfaces
7 interfaces between chains.
- A–B · 1105 Ų buried · 21 hydrogen bonds · protein-protein
- A–T · 1007 Ų buried · 17 hydrogen bonds · protein-nucleic
- B–U · 866 Ų buried · 18 hydrogen bonds · protein-nucleic
- A–P · 599 Ų buried · 18 hydrogen bonds · protein-nucleic
- B–Q · 597 Ų buried · 18 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 4 modified (nucleotide modification).
Compared structures
- 3IN5 · Structure of human DNA polymerase kappa inserting dATP opposite an 8-oxoG DNA lesion · the same entry in another collection · chain U against U, 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 3IN5 · PDBe 3IN5 · UniProt Q9UBT6
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