Research workbench
Structure of ABDB/EXD complex bound to a 'MAGENTA14' DNA sequence
Analyse Structure of ABDB/EXD complex bound to a 'MAGENTA14' DNA sequence in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5ZJR
- Type
- protein + DNA
- Length
- 166 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Homeobox protein abdominal-B; Homeobox protein extradenticle; DNA…
- UniProt
- P09087, P40427
- Pockets
- 3 · best druggability 0.72
Structure
x-ray diffraction · 4 distinct chains · 59% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Homeobox protein abdominal-B | protein | 64 | 64% helix, 0% strand | P09087 |
| B | Homeobox protein extradenticle | protein | 74 | 55% helix, 0% strand | P40427 |
| C | DNA (5'-D(*GP*TP*CP*GP*TP*AP*AP*AP*TP*CP*AP*TP*GP*C)-3') | dna | 14 | — | — |
| D | DNA (5'-D(P*GP*CP*AP*TP*GP*AP*TP*TP*TP*AP*CP*GP*AP*C)-3') | dna | 14 | — | — |
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 | 628 | 0.72 | 0.79 | 53 | empty |
| 2 | 123 | 0.44 | 0.77 | 21 | empty |
| 3 | 57 | 0.31 | 0.76 | 13 | empty |
Interfaces
6 interfaces between chains.
- C–D · 627 Ų buried · 68 hydrogen bonds · nucleic-nucleic
- B–D · 613 Ų buried · 13 hydrogen bonds · protein-nucleic
- A–D · 566 Ų buried · 14 hydrogen bonds · protein-nucleic
- B–C · 523 Ų buried · 7 hydrogen bonds · protein-nucleic
- A–C · 418 Ų buried · 7 hydrogen bonds · protein-nucleic
Compared structures
- 5ZJR · Structure of AbdB/Exd complex bound to a 'Magenta14' DNA sequence · the same entry in another collection · chain A against A, TM-score 1.00
- P09087 · AlphaFold monomer V2.0 prediction for homeobox protein abdominal-B (P09087) · a predicted model of the same protein · chain A against A, TM-score 0.90
- P40427 · AlphaFold monomer V2.0 prediction for homeobox protein extradenticle (P40427) · a predicted model of the same protein · chain B against A, TM-score 0.85
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 P09087
- Every structure of UniProt P40427
- Elsewhere: RCSB PDB 5ZJR · PDBe 5ZJR · UniProt P09087 · UniProt P40427
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