MolNFT v1 · #127076 · protein
Crystal structure of human PCNA in complex with ZRANB3 apim motif peptide
5MLW · Proliferating cell nuclear antigen: “Crystal structure of human PCNA in complex with ZRANB3 apim motif peptide”. X-ray diffraction, 1 ligand (SO4), 9 pockets (best druggability 0.37). MolNFT v1 #127076 on GenesisL1: 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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