Research workbench
Antphd with 15BP DNA duplex S-monothioated at cytidine-8
Analyse Antphd with 15BP DNA duplex S-monothioated at cytidine-8 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5JLX
- Type
- protein + DNA
- Length
- 175 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Homeotic protein antennapedia; DNA (5'-D(*AP*GP*AP*AP*AP*GP*CP*(C7S)…
- UniProt
- P02833
- Ligands
- NI
- Pockets
- 4 · best druggability 0.59
Structure
x-ray diffraction · 4 distinct chains · 70% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Homeotic protein antennapedia | protein | 57 | 68% helix, 0% strand | P02833 |
| B, E | DNA (5'-D(*AP*GP*AP*AP*AP*GP*CP*(C7S) P*AP*TP*TP*AP*GP*AP*G)-3') | dna | 15 | — | — |
| C, F | DNA (5'-D(*TP*CP*TP*CP*TP*AP*AP*TP*GP*GP*CP*TP*TP*TP*C)- 3') | dna | 15 | — | — |
| D | Homeotic protein antennapedia | protein | 58 | 71% helix, 0% strand | P02833 |
Ligands and binding sites
- NI · Nickel (II) ion · metal · 3 copies · chains A, D, B, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 51 | 0.59 | 0.92 | 18 | empty |
| 2 | 244 | 0.53 | 0.77 | 29 | empty |
| 3 | 141 | 0.49 | 0.78 | 17 | empty |
| 4 | 74 | 0.37 | 0.78 | 11 | empty |
Interfaces
7 interfaces between chains.
- B–C · 627 Ų buried · 61 hydrogen bonds · nucleic-nucleic
- E–F · 622 Ų buried · 58 hydrogen bonds · nucleic-nucleic
- A–B · 561 Ų buried · 9 hydrogen bonds · protein-nucleic
- D–E · 542 Ų buried · 8 hydrogen bonds · protein-nucleic
- A–D · 489 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (nucleotide modification).
Compared structures
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 P02833
- Elsewhere: RCSB PDB 5JLX · PDBe 5JLX · UniProt P02833
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.