MolNFT v1 · #107338 · protein + DNA
Structure of DNA polymerase kappa in complex with benzopyrene adducted DNA
4U7C: “Structure of DNA polymerase kappa in complex with benzopyrene adducted DNA”. X-ray diffraction, 3 ligands (VKJ, 0KX, MG), 9 pockets (best druggability 0.81). MolNFT v1 #107338 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 4U7C
- Type
- protein + DNA
- Length
- 903 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
- VKJ, 0KX, MG
- Pockets
- 9 · best druggability 0.81
Structure
x-ray diffraction · 4 distinct chains · 50% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase kappa (EC 2.7.7.7) | protein | 431 | 50% helix, 19% strand | Q9UBT6 |
| B | DNA polymerase kappa (EC 2.7.7.7) | protein | 430 | 50% helix, 20% 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(*P*AP*TP*GP*(VKJ)P*CP*TP*GP*AP*TP*CP*CP*GP*C)- 3') | dna | 12 | — | — |
Ligands and binding sites
- VKJ · 2'-deoxy-N-[(7R,8S,9R,10S)-7,8,9-trihydroxy-7,8,9,10-tetrahydrobenzo[pqr]tetraphen-10-yl]guanosine 5'-(dihydrogen phosphate) · ligand · 2 copies · chains A, C, D, B, P, T
- 0KX · 2'-deoxy-5'-O-[(R)-hydroxy{[(r)-hydroxy(phosphonooxy) phosphoryl]amino}phosphoryl]cytidine · ligand · 2 copies · chains A, C, B, P
- MG · Magnesium ion · metal · 2 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · 3 copies · chains A, C, B, T
- EDO · 1,2-ethanediol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 743 | 0.81 | 0.85 | 80 | PEG |
| 2 | 760 | 0.79 | 0.83 | 78 | empty |
| 3 | 722 | 0.72 | 0.79 | 46 | empty |
| 4 | 665 | 0.72 | 0.79 | 52 | empty |
| 5 | 307 | 0.58 | 0.77 | 33 | MG, 0KX |
Interfaces
9 interfaces between chains.
- A–B · 1522 Ų buried · 39 hydrogen bonds · protein-protein
- A–D · 926 Ų buried · 21 hydrogen bonds · protein-nucleic
- B–T · 924 Ų buried · 19 hydrogen bonds · protein-nucleic
- B–P · 654 Ų buried · 19 hydrogen bonds · protein-nucleic
- A–C · 646 Ų buried · 20 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 4 covalent (covalent ligand).
Compared structures
- 4U7C · Structure of DNA polymerase kappa in complex with benzopyrene adducted DNA · 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 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 4U7C · PDBe 4U7C · UniProt Q9UBT6
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