Research workbench
Crystal structure of human PCNA in complex with ZRANB3 apim motif peptide
Analyse Crystal structure of human PCNA in complex with ZRANB3 apim motif peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5MLW
- Type
- protein
- Length
- 786 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Proliferating cell nuclear antigen; Apim motif peptide
- UniProt
- P12004
- Ligands
- SO4
- Pockets
- 9 · best druggability 0.37
Structure
x-ray diffraction · 5 distinct chains · 19% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Proliferating cell nuclear antigen | protein | 253 | 19% helix, 47% strand | P12004 |
| B, D | Apim motif peptide | protein | 11 | 27% helix, 9% strand | — |
| C | Proliferating cell nuclear antigen | protein | 248 | 19% helix, 47% strand | P12004 |
| E | Proliferating cell nuclear antigen | protein | 253 | 19% helix, 47% strand | P12004 |
| F | Apim motif peptide | protein | 10 | 30% helix, 20% strand | — |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 7 copies · chains A, C, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 88 | 0.37 | 0.76 | 25 | empty |
| 2 | 83 | 0.37 | 0.76 | 19 | empty |
| 3 | 98 | 0.37 | 0.75 | 20 | empty |
| 4 | 82 | 0.36 | 0.76 | 20 | empty |
| 5 | 76 | 0.34 | 0.75 | 18 | empty |
Interfaces
6 interfaces between chains.
- A–E · 738 Ų buried · 15 hydrogen bonds · protein-protein
- A–C · 729 Ų buried · 14 hydrogen bonds · protein-protein
- C–E · 719 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 632 Ų buried · 6 hydrogen bonds · protein-protein
- E–F · 624 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 5MLW · Crystal structure of human PCNA in complex with ZRANB3 APIM motif 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 5MLW · PDBe 5MLW · UniProt P12004
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