Research workbench
Crystal structure of human PCNA in complex with ZRANB3 pip box peptide
Analyse Crystal structure of human PCNA in complex with ZRANB3 pip box peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5MLO
- Type
- protein
- Length
- 797 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Proliferating cell nuclear antigen; ZRANB3 pip box peptide
- UniProt
- P12004
- Ligands
- NA
- Pockets
- 6 · best druggability 0.46
Structure
x-ray diffraction · 4 distinct chains · 21% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E | Proliferating cell nuclear antigen | protein | 255 | 19% helix, 46% strand | P12004 |
| B | ZRANB3 pip box peptide | protein | 10 | 30% helix, 10% strand | — |
| D | ZRANB3 pip box peptide | protein | 11 | 36% helix, 9% strand | — |
| F | ZRANB3 pip box peptide | protein | 11 | 36% helix, 9% strand | — |
Ligands and binding sites
- NA · Sodium ion · metal · 4 copies · chains A, C, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 50 | 0.46 | 0.84 | 14 | empty |
| 2 | 126 | 0.44 | 0.77 | 27 | empty |
| 3 | 83 | 0.35 | 0.75 | 19 | empty |
| 4 | 82 | 0.33 | 0.74 | 16 | empty |
| 5 | 63 | 0.31 | 0.75 | 17 | empty |
Interfaces
6 interfaces between chains.
- C–E · 779 Ų buried · 19 hydrogen bonds · protein-protein
- A–C · 777 Ų buried · 16 hydrogen bonds · protein-protein
- A–E · 729 Ų buried · 14 hydrogen bonds · protein-protein
- C–D · 717 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 665 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 5MLO · Crystal structure of human PCNA in complex with ZRANB3 PIP box peptide · 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 5MLO · PDBe 5MLO · UniProt P12004
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