Research workbench
Crystal structure analysis of PCNA from thermococcus kodakaraensis TK0582
Analyse Crystal structure analysis of PCNA from thermococcus kodakaraensis TK0582 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3LX2
- Type
- protein
- Length
- 739 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase sliding clamp 2
- UniProt
- Q5JFD3
- Ligands
- SO4
- Pockets
- 13 · best druggability 0.55
Structure
x-ray diffraction · 2 distinct chains · 18% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase sliding clamp 2 | protein | 247 | 18% helix, 45% strand | Q5JFD3 |
| B, C | DNA polymerase sliding clamp 2 | protein | 246 | 18% helix, 46% strand | Q5JFD3 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 6 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 126 | 0.55 | 0.82 | 23 | empty |
| 2 | 134 | 0.54 | 0.81 | 19 | empty |
| 3 | 71 | 0.51 | 0.86 | 19 | empty |
| 4 | 114 | 0.51 | 0.81 | 19 | empty |
| 5 | 103 | 0.43 | 0.78 | 22 | empty |
Interfaces
3 interfaces between chains.
- B–C · 769 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 726 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 704 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 3LX2 · Crystal Structure analysis of PCNA from Thermococcus kodakaraensis tk0582 · the same entry in another collection · chain A against A, TM-score 1.00
- Q5JFD3 · AlphaFold monomer V2.0 prediction for DNA polymerase sliding clamp 2 (Q5JFD3) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 Q5JFD3
- Elsewhere: RCSB PDB 3LX2 · PDBe 3LX2 · UniProt Q5JFD3
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