MolNFT v1 · #127068 · protein
Crystal structure of human PCNA in complex with ZRANB3 pip box peptide
5MLO · Proliferating cell nuclear antigen: “Crystal structure of human PCNA in complex with ZRANB3 pip box peptide”. X-ray diffraction, 1 ligand (NA), 6 pockets (best druggability 0.46). MolNFT v1 #127068 on GenesisL1: 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
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.