Research workbench
Crystal structure of human PCNA in complex with the pip box of DVC1
Analyse Crystal structure of human PCNA in complex with the pip box of DVC1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5IY4
- Type
- protein
- Length
- 790 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Proliferating cell nuclear antigen; DVC1 pip box
- UniProt
- P12004
- Pockets
- 4 · best druggability 0.45
Structure
x-ray diffraction · 4 distinct chains · 18% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E | Proliferating cell nuclear antigen | protein | 250 | 19% helix, 47% strand | P12004 |
| B, D | DVC1 pip box | protein | 14 | 21% helix, 7% strand | — |
| C | Proliferating cell nuclear antigen | protein | 251 | 18% helix, 47% strand | P12004 |
| F | DVC1 pip box | protein | 11 | 0% helix, 0% strand | — |
Pockets
4 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 89 | 0.45 | 0.80 | 18 | empty |
| 2 | 79 | 0.38 | 0.77 | 16 | empty |
| 3 | 71 | 0.35 | 0.76 | 18 | empty |
| 4 | 54 | 0.27 | 0.74 | 15 | empty |
Interfaces
6 interfaces between chains.
- C–D · 802 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 788 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 775 Ų buried · 17 hydrogen bonds · protein-protein
- A–E · 743 Ų buried · 16 hydrogen bonds · protein-protein
- C–E · 726 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 5IY4 · Crystal structure of human PCNA in complex with the PIP box of DVC1 · 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 5IY4 · PDBe 5IY4 · UniProt P12004
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