MolNFT v1 · #68733 · protein + DNA
Eukaryotic sliding clamp PCNA bound to DNA
3K4X · Proliferating cell nuclear antigen: “Eukaryotic sliding clamp PCNA bound to DNA”. X-ray diffraction, 9 pockets (best druggability 0.77). MolNFT v1 #68733 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3K4X
- Type
- protein + DNA
- Length
- 778 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Proliferating cell nuclear antigen; DNA (5'-D(*CP*CP*CP*AP*TP*CP*GP*TP*AP*T)-3'); DNA…
- UniProt
- P15873
- Pockets
- 9 · best druggability 0.77
Structure
x-ray diffraction · 3 distinct chains · 19% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Proliferating cell nuclear antigen | protein | 758 | 19% helix, 45% strand | P15873 |
| B | DNA (5'-D(*CP*CP*CP*AP*TP*CP*GP*TP*AP*T)-3') | dna | 10 | — | — |
| C | DNA (5'-D(*TP*TP*TP*TP*AP*TP*AP*CP*GP*AP*TP*GP*GP*G)-3') | dna | 10 | — | — |
Pockets
9 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 468 | 0.77 | 0.86 | 39 | empty |
| 2 | 476 | 0.65 | 0.78 | 45 | empty |
| 3 | 155 | 0.44 | 0.75 | 22 | empty |
| 4 | 160 | 0.43 | 0.74 | 29 | empty |
| 5 | 96 | 0.36 | 0.75 | 14 | empty |
Interfaces
3 interfaces between chains.
- A–B · 474 Ų buried · 4 hydrogen bonds · protein-nucleic
- B–C · 461 Ų buried · 33 hydrogen bonds · nucleic-nucleic
- A–C · 218 Ų buried · 2 hydrogen bonds · protein-nucleic
Compared structures
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 P15873
- Elsewhere: RCSB PDB 3K4X · PDBe 3K4X · UniProt P15873
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