MolNFT v1 · #57190 · protein + DNA
Crystal structure of aristaless and clawless homeodomains bound to DNA
3A01 · Homeodomain-containing protein: “Crystal structure of aristaless and clawless homeodomains bound to DNA”. X-ray diffraction, 9 pockets (best druggability 0.74). MolNFT v1 #57190 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 3A01
- Type
- protein + DNA
- Length
- 332 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Homeodomain-containing protein; Homeobox protein aristaless…
- UniProt
- Q9VD99, Q06453
- Pockets
- 9 · best druggability 0.74
Structure
x-ray diffraction · 6 distinct chains · 64% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Homeodomain-containing protein | protein | 78 | 53% helix, 0% strand | Q9VD99 |
| B | Homeobox protein aristaless | protein | 57 | 70% helix, 0% strand | Q06453 |
| C, G | 5'-D(*GP*GP*CP*TP*TP*AP*AP*TP*TP*AP*AP*TP*TP*GP*CP*GP*G)- 3' | dna | 17 | — | — |
| D, H | 5'-D(*CP*CP*GP*CP*AP*AP*TP*TP*AP*AP*TP*TP*AP*AP*GP*CP*C)- 3' | dna | 17 | — | — |
| E | Homeodomain-containing protein | protein | 68 | 68% helix, 0% strand | Q9VD99 |
| F | Homeobox protein aristaless | protein | 61 | 69% helix, 0% strand | Q06453 |
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 514 | 0.74 | 0.83 | 50 | empty |
| 2 | 277 | 0.71 | 0.86 | 27 | empty |
| 3 | 364 | 0.66 | 0.81 | 47 | empty |
| 4 | 450 | 0.64 | 0.78 | 41 | empty |
| 5 | 76 | 0.43 | 0.81 | 16 | empty |
Interfaces
16 interfaces between chains.
- C–D · 753 Ų buried · 75 hydrogen bonds · nucleic-nucleic
- G–H · 745 Ų buried · 76 hydrogen bonds · nucleic-nucleic
- A–D · 714 Ų buried · 14 hydrogen bonds · protein-nucleic
- A–C · 678 Ų buried · 15 hydrogen bonds · protein-nucleic
- E–G · 649 Ų buried · 14 hydrogen bonds · protein-nucleic
Compared structures
- 3A01 · Crystal structure of Aristaless and Clawless homeodomains bound to DNA · the same entry in another collection · chain H against H, TM-score 1.00
- Q06453 · AlphaFold monomer V2.0 prediction for homeobox protein aristaless (Q06453) · a predicted model of the same protein · chain B against A, TM-score 0.95
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 Q9VD99
- Every structure of UniProt Q06453
- Elsewhere: RCSB PDB 3A01 · PDBe 3A01 · UniProt Q9VD99 · UniProt Q06453
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