MolNFT v1 · #122731 · protein
Crystal structure of human PCNA in complex with the pip box of DVC1
5IY4 · Proliferating cell nuclear antigen: “Crystal structure of human PCNA in complex with the pip box of DVC1”. X-ray diffraction, 4 pockets (best druggability 0.45). MolNFT v1 #122731 on GenesisL1: 3D structure, binding sites and…
- 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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