Research workbench
Crystal structure of proliferating cell nuclear antigen from leishmania donovani at 2.73 ångström resolution
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
- 5H0T
- Type
- protein
- Length
- 1,488 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Proliferating cell nuclear antigen
- UniProt
- B5TV91
- Pockets
- 10 · best druggability 0.69
Structure
x-ray diffraction · 1 distinct chain · 19% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D, E, B, C, F | Proliferating cell nuclear antigen | protein | 248 | 19% helix, 46% strand | B5TV91 |
Ligands and binding sites
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains A, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 848 | 0.69 | 0.75 | 86 | empty |
| 2 | 202 | 0.64 | 0.84 | 32 | PEG |
| 3 | 381 | 0.61 | 0.77 | 37 | empty |
| 4 | 356 | 0.56 | 0.75 | 45 | empty |
| 5 | 166 | 0.43 | 0.74 | 21 | empty |
Interfaces
11 interfaces between chains.
- D–F · 657 Ų buried · 13 hydrogen bonds · protein-protein
- B–C · 653 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 649 Ų buried · 13 hydrogen bonds · protein-protein
- D–E · 643 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 629 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 5H0T · Crystal structure of proliferating cell nuclear antigen from Leishmania donovani at 2.73… · 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 5H0T · PDBe 5H0T · UniProt B5TV91
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