Research workbench
Crystal structure of SCINO2P-SCINO4P bound promoter DNA
Analyse Crystal structure of SCINO2P-SCINO4P bound promoter DNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7XQ5
- Type
- protein + DNA
- Length
- 178 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein INO4; Protein INO2; DNA (5'-D(P*CP*CP*TP*GP*CP*AP*TP*GP*TP*GP*AP*AP*AP*AP*T)…
- UniProt
- P13902, P26798
- Pockets
- 4 · best druggability 0.79
Structure
x-ray diffraction · 4 distinct chains · 80% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein INO4 | protein | 75 | 81% helix, 0% strand | P13902 |
| B | Protein INO2 | protein | 73 | 79% helix, 0% strand | P26798 |
| C | DNA (5'-D(P*CP*CP*TP*GP*CP*AP*TP*GP*TP*GP*AP*AP*AP*AP*T)- 3') | dna | 15 | — | — |
| D | DNA (5'-D(*GP*AP*TP*TP*TP*TP*CP*AP*CP*AP*TP*GP*CP*AP*G)- 3') | dna | 15 | — | — |
Ligands and binding sites
- HEZ · Hexane-1,6-diol · additive · 3 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 405 | 0.79 | 0.88 | 37 | empty |
| 2 | 150 | 0.48 | 0.77 | 17 | empty |
| 3 | 85 | 0.33 | 0.74 | 15 | empty |
| 4 | 63 | 0.33 | 0.76 | 15 | empty |
Interfaces
6 interfaces between chains.
- A–B · 1307 Ų buried · 7 hydrogen bonds · protein-protein
- C–D · 636 Ų buried · 57 hydrogen bonds · nucleic-nucleic
- B–D · 516 Ų buried · 7 hydrogen bonds · protein-nucleic
- B–C · 468 Ų buried · 6 hydrogen bonds · protein-nucleic
- A–C · 439 Ų buried · 11 hydrogen bonds · protein-nucleic
Compared structures
- 7XQ5 · Crystal structure of ScIno2p-ScIno4p bound promoter DNA · the same entry in another collection · chain A against A, TM-score 1.00
- P26798 · AlphaFold monomer V2.0 prediction for protein INO2 (P26798) · a predicted model of the same protein · chain B against A, TM-score 0.93
- P13902 · AlphaFold monomer V2.0 prediction for protein INO4 (P13902) · a predicted model of the same protein · chain A against A, TM-score 0.92
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 P13902
- Every structure of UniProt P26798
- Elsewhere: RCSB PDB 7XQ5 · PDBe 7XQ5 · UniProt P13902 · UniProt P26798
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.