MolNFT v1 · #108040 · protein + DNA
Crystal structure of a ubx-exd-DNA complex including the ubda motif
4UUS · Homeotic protein ultrabithorax: “Crystal structure of a ubx-exd-DNA complex including the ubda motif”. X-ray diffraction, 6 pockets (best druggability 0.78). MolNFT v1 #108040 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 4UUS
- Type
- protein + DNA
- Length
- 327 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Homeotic protein ultrabithorax; Homeotic protein extradenticle…
- UniProt
- P83949, P40427
- Pockets
- 6 · best druggability 0.78
Structure
x-ray diffraction · 6 distinct chains · 75% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Homeotic protein ultrabithorax | protein | 67 | 78% helix, 0% strand | P83949 |
| B | Homeotic protein extradenticle | protein | 69 | 75% helix, 0% strand | P40427 |
| C, G | 5'-D(*GP*TP*CP*GP*CP*CP*AP*TP*AP*AP*AP*TP*CP*AP*C)-3' | dna | 15 | — | — |
| D, H | 5'-D(*AP*CP*GP*TP*GP*AP*TP*TP*TP*AP*TP*GP*GP*CP*G)-3' | dna | 15 | — | — |
| E | Homeotic protein ultrabithorax | protein | 65 | 72% helix, 0% strand | P83949 |
| F | Homeotic protein extradenticle | protein | 66 | 73% helix, 0% strand | P40427 |
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 852 | 0.78 | 0.81 | 76 | empty |
| 2 | 903 | 0.76 | 0.80 | 79 | empty |
| 3 | 213 | 0.57 | 0.80 | 25 | empty |
| 4 | 152 | 0.53 | 0.80 | 22 | empty |
| 5 | 74 | 0.38 | 0.78 | 13 | empty |
Interfaces
16 interfaces between chains.
- A–F · 866 Ų buried · 6 hydrogen bonds · protein-protein
- C–D · 615 Ų buried · 65 hydrogen bonds · nucleic-nucleic
- G–H · 606 Ų buried · 56 hydrogen bonds · nucleic-nucleic
- A–C · 542 Ų buried · 10 hydrogen bonds · protein-nucleic
- E–H · 481 Ų buried · 16 hydrogen bonds · protein-nucleic
Compared structures
- 4UUS · Crystal structure of a ubx-exd-DNA complex including the ubda motif · the same entry in another collection · chain H against H, TM-score 1.00
- P83949 · AlphaFold monomer V2.0 prediction for homeotic protein ultrabithorax (P83949) · a predicted model of the same protein · chain A against A, TM-score 0.98
- P40427 · AlphaFold monomer V2.0 prediction for homeobox protein extradenticle (P40427) · a predicted model of the same protein · chain B against A, TM-score 0.92
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 P83949
- Every structure of UniProt P40427
- Elsewhere: RCSB PDB 4UUS · PDBe 4UUS · UniProt P83949 · UniProt P40427
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