Research workbench
Crystal structure of proliferating cell nuclear antigen (PCNA) homolog from sulfolobus tokodaii
Analyse Crystal structure of proliferating cell nuclear antigen (PCNA) homolog from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1UD9
- Type
- protein
- Length
- 960 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase sliding clamp a
- UniProt
- Q975N2
- Ligands
- ZN
- Pockets
- 11 · best druggability 0.82
Structure
x-ray diffraction · 4 distinct chains · 22% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase sliding clamp a | protein | 242 | 24% helix, 44% strand | Q975N2 |
| B | DNA polymerase sliding clamp a | protein | 238 | 21% helix, 47% strand | Q975N2 |
| C | DNA polymerase sliding clamp a | protein | 239 | 22% helix, 44% strand | Q975N2 |
| D | DNA polymerase sliding clamp a | protein | 241 | 21% helix, 44% strand | Q975N2 |
Ligands and binding sites
- ZN · Zinc ion · metal · 23 copies · chains A, D, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 148 | 0.82 | 0.97 | 28 | empty |
| 2 | 86 | 0.78 | 0.98 | 24 | empty |
| 3 | 81 | 0.78 | 0.98 | 21 | empty |
| 4 | 60 | 0.75 | 0.98 | 19 | empty |
| 5 | 92 | 0.43 | 0.79 | 18 | empty |
Interfaces
4 interfaces between chains.
- B–C · 606 Ų buried · 10 hydrogen bonds · protein-protein
- C–D · 261 Ų buried · 3 hydrogen bonds · protein-protein
- A–D · 152 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 19 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 1UD9 · Crystal Structure of Proliferating Cell Nuclear Antigen (PCNA) Homolog From Sulfolobus… · the same entry in another collection · chain D against D, TM-score 1.00
- Q975N2 · AlphaFold monomer V2.0 prediction for DNA polymerase sliding clamp 1 (Q975N2) · 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 Q975N2
- Elsewhere: RCSB PDB 1UD9 · PDBe 1UD9 · UniProt Q975N2
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