MolNFT v1 · #88547 · protein + DNA
Crystal structure of a ubx-exd-DNA complex including the hexapeptide and ubda motifs
4CYC · Homeotic protein ultrabithorax: “Crystal structure of a ubx-exd-DNA complex including the hexapeptide and ubda motifs”. X-ray diffraction, 4 pockets (best druggability 0.70). MolNFT v1 #88547 on GenesisL1: 3D structure, binding…
- PDB
- 4CYC
- Type
- protein + DNA
- Length
- 154 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Homeotic protein ultrabithorax; Homeobox protein extradenticle…
- UniProt
- P83949, P40427
- Pockets
- 4 · best druggability 0.70
Structure
x-ray diffraction · 4 distinct chains · 71% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Homeotic protein ultrabithorax | protein | 66 | 71% helix, 0% strand | P83949 |
| B | Homeobox protein extradenticle | protein | 58 | 71% helix, 0% strand | P40427 |
| C | 5'-D(*GP*TP*CP*GP*CP*CP*AP*TP*AP*AP*AP*TP*CP*AP*CP)-3' | dna | 15 | — | — |
| D | 5'-D(*AP*CP*GP*TP*GP*AP*TP*TP*TP*AP*TP*GP*GP*CP*GP)-3' | dna | 15 | — | — |
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 | 388 | 0.70 | 0.83 | 45 | empty |
| 2 | 101 | 0.37 | 0.75 | 14 | empty |
| 3 | 52 | 0.34 | 0.79 | 12 | empty |
| 4 | 57 | 0.24 | 0.72 | 13 | empty |
Interfaces
6 interfaces between chains.
- C–D · 622 Ų buried · 62 hydrogen bonds · nucleic-nucleic
- A–C · 558 Ų buried · 8 hydrogen bonds · protein-nucleic
- A–D · 433 Ų buried · 12 hydrogen bonds · protein-nucleic
- B–D · 418 Ų buried · 10 hydrogen bonds · protein-nucleic
- B–C · 396 Ų buried · 7 hydrogen bonds · protein-nucleic
Compared structures
- 4CYC · Crystal structure of a ubx-exd-DNA complex including the hexapeptide and ubda motifs · the same entry in another collection · chain A against A, 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 0.97
- P83949 · AlphaFold monomer V2.0 prediction for homeotic protein ultrabithorax (P83949) · a predicted model of the same protein · chain A against A, TM-score 0.93
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 4CYC · PDBe 4CYC · UniProt P83949 · UniProt P40427
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