Research workbench
Crystal structure of proliferating cell nuclear antigen from leishmania donovani with an unexplained density near residues PRO229, PR0267 and ALA285
Analyse Crystal structure of proliferating cell nuclear antigen from leishmania… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6J0J
- Type
- protein
- Length
- 1,501 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Proliferating cell nuclear antigen
- UniProt
- B5TV91
- Pockets
- 11 · best druggability 0.68
Structure
x-ray diffraction · 3 distinct chains · 19% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, F | Proliferating cell nuclear antigen | protein | 248 | 20% helix, 44% strand | B5TV91 |
| D | Proliferating cell nuclear antigen | protein | 251 | 19% helix, 45% strand | B5TV91 |
| E | Proliferating cell nuclear antigen | protein | 258 | 19% helix, 43% strand | B5TV91 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 767 | 0.68 | 0.75 | 81 | empty |
| 2 | 425 | 0.65 | 0.78 | 60 | PEG |
| 3 | 404 | 0.60 | 0.76 | 34 | empty |
| 4 | 153 | 0.43 | 0.75 | 21 | empty |
| 5 | 65 | 0.36 | 0.78 | 14 | empty |
Interfaces
11 interfaces between chains.
- D–F · 708 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 688 Ų buried · 14 hydrogen bonds · protein-protein
- D–E · 671 Ų buried · 13 hydrogen bonds · protein-protein
- E–F · 641 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 640 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 6J0J · Crystal structure of Proliferating Cell Nuclear Antigen from Leishmania donovani with an… · 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 B5TV91
- Elsewhere: RCSB PDB 6J0J · PDBe 6J0J · UniProt B5TV91
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