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Crystal structure of the complex of proliferating cell nuclear antigen (PCNA) from leishmania donovani with 1,5-bis (4-amidinophenoxy) pentane (pnt) at 2.95 a resolution
Analyse Crystal structure of the complex of proliferating cell nuclear antigen (PCNA)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7WP3
- 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
- Ligands
- PNT
- Pockets
- 15 · best druggability 0.69
Structure
x-ray diffraction · 1 distinct chain · 18% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Proliferating cell nuclear antigen | protein | 248 | 18% helix, 45% strand | B5TV91 |
Ligands and binding sites
- PNT · 1,5-bis(4-amidinophenoxy)pentane · ligand · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 555 | 0.69 | 0.78 | 66 | empty |
| 2 | 506 | 0.62 | 0.75 | 59 | empty |
| 3 | 304 | 0.55 | 0.76 | 34 | empty |
| 4 | 298 | 0.54 | 0.75 | 37 | empty |
| 5 | 66 | 0.41 | 0.80 | 13 | empty |
Interfaces
11 interfaces between chains.
- A–D · 678 Ų buried · 16 hydrogen bonds · protein-protein
- B–C · 676 Ų buried · 15 hydrogen bonds · protein-protein
- B–F · 672 Ų buried · 13 hydrogen bonds · protein-protein
- D–E · 657 Ų buried · 18 hydrogen bonds · protein-protein
- A–E · 643 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 7WP3 · Crystal structure of the complex of proliferating cell nuclear antigen (PCNA) from… · 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 7WP3 · PDBe 7WP3 · UniProt B5TV91
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