Research workbench
Crystal structure of PCNA in complex with DNA polymerase kappa fragment
Analyse Crystal structure of PCNA in complex with DNA polymerase kappa fragment in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2ZVL
- Type
- protein
- Length
- 1,543 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Proliferating cell nuclear antigen; DNA polymerase kappa
- EC
- 2.7.7.7
- UniProt
- P12004
- Ligands
- ZN, SO4
- Pockets
- 10 · best druggability 0.44
Structure
x-ray diffraction · 8 distinct chains · 19% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Proliferating cell nuclear antigen | protein | 245 | 20% helix, 47% strand | P12004 |
| U, Z | DNA polymerase kappa (EC 2.7.7.7) | protein | 11 | 0% helix, 18% strand | — |
| B, C, D | Proliferating cell nuclear antigen | protein | 247 | 19% helix, 48% strand | P12004 |
| V, Y | DNA polymerase kappa (EC 2.7.7.7) | protein | 13 | 23% helix, 0% strand | — |
| W | DNA polymerase kappa (EC 2.7.7.7) | protein | 12 | 0% helix, 8% strand | — |
| X | DNA polymerase kappa (EC 2.7.7.7) | protein | 10 | 30% helix, 10% strand | — |
| E | Proliferating cell nuclear antigen | protein | 244 | 18% helix, 48% strand | P12004 |
| F | Proliferating cell nuclear antigen | protein | 243 | 19% helix, 48% strand | P12004 |
Ligands and binding sites
- ZN · Zinc ion · metal · 6 copies · chains B, V, C, W, E, Y, F, Z
- SO4 · Sulfate ion · ion · 4 copies · chains A, C, F, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 129 | 0.44 | 0.77 | 27 | empty |
| 2 | 93 | 0.37 | 0.76 | 20 | empty |
| 3 | 91 | 0.35 | 0.75 | 16 | empty |
| 4 | 59 | 0.33 | 0.77 | 15 | empty |
| 5 | 72 | 0.33 | 0.75 | 15 | empty |
Interfaces
12 interfaces between chains.
- E–F · 736 Ų buried · 14 hydrogen bonds · protein-protein
- D–F · 735 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 727 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 713 Ų buried · 10 hydrogen bonds · protein-protein
- D–E · 704 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 2ZVL · Crystal structure of PCNA in complex with DNA polymerase kappa fragment · the same entry in another collection · chain A against A, TM-score 1.00
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
- Elsewhere: RCSB PDB 2ZVL · PDBe 2ZVL · UniProt P12004
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