Research workbench
Structure of the homeotic UBX/EXD/DNA ternary complex
Analyse Structure of the homeotic UBX/EXD/DNA ternary complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1B8I
- Type
- protein + DNA
- Length
- 150 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (5'-D(*GP*TP*CP*GP*CP*CP*AP*TP*AP*AP*AP*TP*CP*AP*C)- 3'); DNA…
- UniProt
- P83949, P40427
- Pockets
- 2 · best druggability 0.76
Structure
x-ray diffraction · 4 distinct chains · 65% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | DNA (5'-D(*GP*TP*CP*GP*CP*CP*AP*TP*AP*AP*AP*TP*CP*AP*C)- 3') | dna | 15 | — | — |
| D | DNA (5'-D(*AP*CP*GP*TP*GP*AP*TP*TP*TP*AP*TP*GP*GP*CP*G)- 3') | dna | 15 | — | — |
| A | Protein (ultrabithorax homeotic protein IV) | protein | 62 | 65% helix, 0% strand | P83949 |
| B | Protein (homeobox protein extradenticle) | protein | 58 | 66% helix, 0% strand | P40427 |
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 454 | 0.76 | 0.85 | 42 | empty |
| 2 | 57 | 0.31 | 0.76 | 10 | empty |
Interfaces
6 interfaces between chains.
- C–D · 627 Ų buried · 65 hydrogen bonds · nucleic-nucleic
- D–A · 483 Ų buried · 19 hydrogen bonds · protein-nucleic
- C–A · 455 Ų buried · 7 hydrogen bonds · protein-nucleic
- D–B · 434 Ų buried · 15 hydrogen bonds · protein-nucleic
- C–B · 398 Ų buried · 5 hydrogen bonds · protein-nucleic
Compared structures
- 1B8I · Structure of the homeotic UBX/EXD/DNA ternary complex · the same entry in another collection · chain C against C, TM-score 1.00
- P40427 · AlphaFold monomer V2.0 prediction for homeobox protein extradenticle (P40427) · a predicted model of the same protein · chain B against A, TM-score 0.96
- P83949 · AlphaFold monomer V2.0 prediction for homeotic protein ultrabithorax (P83949) · a predicted model of the same protein · chain A against A, TM-score 0.90
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 P83949
- Every structure of UniProt P40427
- Elsewhere: RCSB PDB 1B8I · PDBe 1B8I · UniProt P83949 · UniProt P40427
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