MolNFT v1 · #183582 · protein + DNA
Human pol kappa holoenzyme with ub-PCNA
7NV1 · Proliferating cell nuclear antigen: “Human pol kappa holoenzyme with ub-PCNA”. Electron microscopy, 1 ligand (TTP), 16 pockets (best druggability 0.80). MolNFT v1 #183582 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7NV1
- Type
- protein + DNA
- Length
- 1,233 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Proliferating cell nuclear antigen; DNA polymerase kappa; DNA primer; DNA template
- EC
- 2.7.7.7
- UniProt
- P12004, Q9UBT6
- Ligands
- TTP
- Pockets
- 16 · best druggability 0.80
Structure
electron microscopy · 6 distinct chains · 22% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Proliferating cell nuclear antigen | protein | 248 | 16% 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 |
| A | DNA polymerase kappa (EC 2.7.7.7) | protein | 430 | 36% helix, 13% strand | Q9UBT6 |
| 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
16 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 625 | 0.80 | 0.85 | 51 | empty |
| 2 | 835 | 0.71 | 0.77 | 57 | empty |
| 3 | 580 | 0.66 | 0.77 | 34 | empty |
| 4 | 228 | 0.65 | 0.83 | 31 | TTP |
| 5 | 300 | 0.65 | 0.81 | 26 | empty |
Interfaces
12 interfaces between chains.
- P–T · 1137 Ų buried · 102 hydrogen bonds · nucleic-nucleic
- A–T · 908 Ų buried · 6 hydrogen bonds · protein-nucleic
- C–D · 773 Ų buried · 19 hydrogen bonds · protein-protein
- B–C · 720 Ų buried · 7 hydrogen bonds · protein-protein
- D–A · 686 Ų buried · 3 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 P12004
- Every structure of UniProt Q9UBT6
- Elsewhere: RCSB PDB 7NV1 · PDBe 7NV1 · UniProt P12004 · UniProt Q9UBT6
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.