MolNFT v1 · #50019 · protein + DNA
Structure of SCR/EXD complex bound to a consensus hox-exd site
2R5Y · DNA (5'- D(*DAP*DCP*DTP*DCP*DTP*DAP*DTP*DGP*DAP*DTP*DTP*DTP*…: “Structure of SCR/EXD complex bound to a consensus hox-exd site”. X-ray diffraction, 3 pockets (best druggability 0.75). MolNFT v1 #50019 on GenesisL1: 3D structure…
- PDB
- 2R5Y
- Type
- protein + DNA
- Length
- 172 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (5'- D(*DAP*DCP*DTP*DCP*DTP*DAP*DTP*DGP*DAP*DTP*DTP*DTP*DAP*DTP*DGP*DGP*DG…
- UniProt
- P09077, P40427
- Pockets
- 3 · best druggability 0.75
Structure
x-ray diffraction · 4 distinct chains · 61% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | DNA (5'- D(*DAP*DCP*DTP*DCP*DTP*DAP*DTP*DGP*DAP*DTP*DTP*DTP*DAP*DTP*DGP*DGP*DG P*DCP*DTP*DG)-3') | dna | 20 | — | — |
| D | DNA (5'- D(*DTP*DCP*DAP*DGP*DCP*DCP*DCP*DAP*DTP*DAP*DAP*DAP*DTP*DCP*DAP*DTP*DA P*DGP*DAP*DG)-3') | dna | 20 | — | — |
| A | Homeotic protein sex combs reduced | protein | 73 | 55% helix, 0% strand | P09077 |
| B | Homeobox protein extradenticle | protein | 59 | 69% helix, 0% strand | P40427 |
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 799 | 0.75 | 0.80 | 66 | empty |
| 2 | 59 | 0.40 | 0.81 | 13 | empty |
| 3 | 118 | 0.35 | 0.73 | 21 | empty |
Interfaces
6 interfaces between chains.
- C–D · 865 Ų buried · 77 hydrogen bonds · nucleic-nucleic
- A–B · 632 Ų buried · 6 hydrogen bonds · protein-protein
- D–A · 629 Ų buried · 14 hydrogen bonds · protein-nucleic
- D–B · 505 Ų buried · 6 hydrogen bonds · protein-nucleic
- C–B · 437 Ų buried · 13 hydrogen bonds · protein-nucleic
Compared structures
- 2R5Y · Structure of Scr/Exd complex bound to a consensus Hox-Exd site · 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
- P09077 · AlphaFold monomer V2.0 prediction for homeotic protein sex combs reduced (P09077) · a predicted model of the same protein · chain A against A, TM-score 0.88
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 P09077
- Every structure of UniProt P40427
- Elsewhere: RCSB PDB 2R5Y · PDBe 2R5Y · UniProt P09077 · UniProt P40427
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