MolNFT v1 · #141807 · protein + DNA
Structure of ABDB/EXD complex bound to a 'RED14' DNA sequence
5ZJQ · Homeobox protein abdominal-B: “Structure of ABDB/EXD complex bound to a 'RED14' DNA sequence”. X-ray diffraction, 3 pockets (best druggability 0.75). MolNFT v1 #141807 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5ZJQ
- Type
- protein + DNA
- Length
- 164 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 0.75
Structure
x-ray diffraction · 4 distinct chains · 63% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Homeobox protein abdominal-B | protein | 63 | 65% helix, 0% strand | P09087 |
| B | Homeobox protein extradenticle | protein | 73 | 60% helix, 0% strand | P40427 |
| C | DNA (5'-D(*GP*TP*CP*AP*TP*AP*AP*AP*TP*CP*AP*TP*GP*C)-3') | dna | 14 | — | — |
| D | DNA (5'-D(*GP*CP*AP*TP*GP*AP*TP*TP*TP*AP*TP*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 | 472 | 0.75 | 0.84 | 47 | empty |
| 2 | 136 | 0.45 | 0.77 | 15 | empty |
| 3 | 57 | 0.28 | 0.75 | 12 | empty |
Interfaces
6 interfaces between chains.
- C–D · 611 Ų buried · 58 hydrogen bonds · nucleic-nucleic
- B–D · 574 Ų buried · 15 hydrogen bonds · protein-nucleic
- B–C · 558 Ų buried · 10 hydrogen bonds · protein-nucleic
- A–D · 503 Ų buried · 15 hydrogen bonds · protein-nucleic
- A–C · 452 Ų buried · 8 hydrogen bonds · protein-nucleic
Compared structures
- 5ZJQ · Structure of AbdB/Exd complex bound to a 'Red14' 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 0.93
- P40427 · AlphaFold monomer V2.0 prediction for homeobox protein extradenticle (P40427) · a predicted model of the same protein · chain B against A, TM-score 0.86
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 5ZJQ · PDBe 5ZJQ · UniProt P09087 · UniProt P40427
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