Research workbench
Human pol kappa holoenzyme with wt PCNA
Analyse Human pol kappa holoenzyme with wt PCNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7NV0
- Type
- protein + DNA
- Length
- 1,233 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase kappa; Proliferating cell nuclear antigen; DNA primer; DNA template
- EC
- 2.7.7.7
- UniProt
- Q9UBT6, P12004
- Ligands
- TTP
- Pockets
- 15 · best druggability 0.80
Structure
electron microscopy · 6 distinct chains · 22% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase kappa (EC 2.7.7.7) | protein | 430 | 36% helix, 13% strand | Q9UBT6 |
| B | Proliferating cell nuclear antigen | protein | 248 | 15% helix, 42% strand | P12004 |
| C | Proliferating cell nuclear antigen | protein | 253 | 13% helix, 43% strand | P12004 |
| D | Proliferating cell nuclear antigen | protein | 249 | 14% helix, 42% strand | P12004 |
| P | DNA primer | dna | 25 | — | — |
| T | DNA template | dna | 28 | — | — |
Ligands and binding sites
- TTP · Thymidine-5'-triphosphate · ligand · chains A, P, T
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 814 | 0.80 | 0.83 | 57 | empty |
| 2 | 444 | 0.69 | 0.80 | 44 | TTP |
| 3 | 379 | 0.65 | 0.80 | 35 | empty |
| 4 | 233 | 0.60 | 0.81 | 21 | empty |
| 5 | 220 | 0.56 | 0.79 | 29 | empty |
Interfaces
12 interfaces between chains.
- P–T · 1138 Ų buried · 102 hydrogen bonds · nucleic-nucleic
- A–T · 902 Ų buried · 6 hydrogen bonds · protein-nucleic
- C–D · 773 Ų buried · 19 hydrogen bonds · protein-protein
- A–D · 743 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 726 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
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
- Every structure of UniProt P12004
- Elsewhere: RCSB PDB 7NV0 · PDBe 7NV0 · UniProt Q9UBT6 · UniProt P12004
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