MolNFT v1 · #153012 · protein
Crystal structure of proliferating cell nuclear antigen from leishmania donovani with an unexplained density near residues PRO229, PR0267 and ALA285
6J0J: “Crystal structure of proliferating cell nuclear antigen from leishmania donovani with an unexplained density…”. X-ray diffraction, 11 pockets (best druggability 0.68). MolNFT v1 #153012 on GenesisL1: 3D structure, binding sites and…
- 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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