Research workbench
Structural and biochemical studies of human PCNA complexes provide the basis for association with CDK/CYCLIN and rationale for inhibitor design
Analyse Structural and biochemical studies of human PCNA complexes provide the basis… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1VYJ
- Type
- protein
- Length
- 1,641 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Proliferating cell nuclear antigen; Small peptide savlqkkitdyfhpkk
- UniProt
- P12004
- Pockets
- 14 · best druggability 0.68
Structure
x-ray diffraction · 3 distinct chains · 18% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, I, K | Proliferating cell nuclear antigen | protein | 257 | 19% helix, 46% strand | P12004 |
| B, D, F, H, J, L | Small peptide savlqkkitdyfhpkk | protein | 16 | 19% helix, 25% strand | — |
| G | Proliferating cell nuclear antigen | protein | 260 | 17% helix, 45% strand | P12004 |
Pockets
14 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 780 | 0.68 | 0.75 | 80 | empty |
| 2 | 474 | 0.60 | 0.75 | 51 | empty |
| 3 | 98 | 0.42 | 0.78 | 18 | empty |
| 4 | 84 | 0.38 | 0.77 | 23 | empty |
| 5 | 77 | 0.38 | 0.78 | 17 | empty |
Interfaces
16 interfaces between chains.
- C–D · 922 Ų buried · 10 hydrogen bonds · protein-protein
- G–H · 898 Ų buried · 8 hydrogen bonds · protein-protein
- K–L · 894 Ų buried · 8 hydrogen bonds · protein-protein
- I–J · 859 Ų buried · 10 hydrogen bonds · protein-protein
- E–F · 857 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide (disulfide).
Compared structures
- 1VYJ · Structural and biochemical studies of human PCNA complexes provide the basis for… · 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 1VYJ · PDBe 1VYJ · UniProt P12004
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