MolNFT v1 · #141810 · protein + DNA
Structure of ABDB/EXD complex bound to a 'BLACK14' DNA sequence
5ZJT · Homeobox protein abdominal-B: “Structure of ABDB/EXD complex bound to a 'BLACK14' DNA sequence”. X-ray diffraction, 6 pockets (best druggability 0.68). MolNFT v1 #141810 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5ZJT
- Type
- protein + DNA
- Length
- 249 residues
- Chains
- 7
- 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
- 6 · best druggability 0.68
Structure
x-ray diffraction · 5 distinct chains · 66% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Homeobox protein abdominal-B | protein | 63 | 68% helix, 0% strand | P09087 |
| B | Homeobox protein extradenticle | protein | 72 | 63% helix, 0% strand | P40427 |
| C, H | DNA (5'-D(*GP*TP*CP*AP*TP*TP*TP*AP*TP*CP*AP*TP*GP*C)-3') | dna | 14 | — | — |
| D, G | DNA (5'-D(*GP*CP*AP*TP*GP*AP*TP*AP*AP*AP*TP*GP*AP*C)-3') | dna | 14 | — | — |
| E | Homeobox protein abdominal-B | protein | 58 | 69% helix, 0% strand | P09087 |
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 438 | 0.68 | 0.80 | 45 | empty |
| 2 | 364 | 0.60 | 0.77 | 42 | empty |
| 3 | 129 | 0.44 | 0.77 | 20 | empty |
| 4 | 71 | 0.35 | 0.77 | 14 | empty |
| 5 | 70 | 0.32 | 0.75 | 12 | empty |
Interfaces
11 interfaces between chains.
- G–H · 623 Ų buried · 61 hydrogen bonds · nucleic-nucleic
- C–D · 607 Ų buried · 59 hydrogen bonds · nucleic-nucleic
- B–D · 582 Ų buried · 9 hydrogen bonds · protein-nucleic
- B–C · 537 Ų buried · 11 hydrogen bonds · protein-nucleic
- E–G · 523 Ų buried · 10 hydrogen bonds · protein-nucleic
Compared structures
- 5ZJT · Structure of AbdB/Exd complex bound to a 'Black14' DNA sequence · the same entry in another collection · chain H against H, TM-score 1.00
- P09087 · AlphaFold monomer V2.0 prediction for homeobox protein abdominal-B (P09087) · a predicted model of the same protein · chain E against A, TM-score 0.95
- P40427 · AlphaFold monomer V2.0 prediction for homeobox protein extradenticle (P40427) · a predicted model of the same protein · chain B against A, TM-score 0.87
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 5ZJT · PDBe 5ZJT · UniProt P09087 · UniProt P40427
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