Research workbench
Crystal structure of anabaena transcription factor hetr complexed with 21-bp DNA from hetp promoter
Analyse Crystal structure of anabaena transcription factor hetr complexed with 21-bp… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4YRV
- Type
- protein + DNA
- Length
- 616 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Heterocyst differentiation control protein; DNA (5'…
- UniProt
- P27709
- Ligands
- CA
- Pockets
- 8 · best druggability 0.81
Structure
x-ray diffraction · 4 distinct chains · 55% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Heterocyst differentiation control protein | protein | 286 | 56% helix, 10% strand | P27709 |
| A | Heterocyst differentiation control protein | protein | 288 | 55% helix, 9% strand | P27709 |
| C | DNA (5'- D(P*GP*CP*GP*AP*GP*GP*GP*GP*TP*CP*TP*AP*AP*CP*CP*CP*CP*TP*CP*AP*T)- 3') | dna | 21 | — | — |
| D | DNA (5'- D(P*AP*TP*GP*AP*GP*GP*GP*GP*TP*TP*AP*GP*AP*CP*CP*CP*CP*TP*CP*GP*C)- 3') | dna | 21 | — | — |
Ligands and binding sites
- CA · Calcium ion · metal · 4 copies · chains B, D, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 832 | 0.81 | 0.84 | 64 | CA |
| 2 | 223 | 0.75 | 0.89 | 23 | empty |
| 3 | 411 | 0.69 | 0.81 | 34 | CA |
| 4 | 407 | 0.67 | 0.80 | 37 | CA |
| 5 | 170 | 0.48 | 0.77 | 31 | empty |
Interfaces
6 interfaces between chains.
- B–A · 7306 Ų buried · 106 hydrogen bonds · protein-protein
- C–D · 957 Ų buried · 99 hydrogen bonds · nucleic-nucleic
- A–C · 592 Ų buried · 15 hydrogen bonds · protein-nucleic
- B–D · 569 Ų buried · 13 hydrogen bonds · protein-nucleic
- B–C · 337 Ų buried · 6 hydrogen bonds · protein-nucleic
Compared structures
- 4YRV · Crystal structure of Anabaena transcription factor HetR complexed with 21-bp DNA from… · the same entry in another collection · chain B against B, TM-score 1.00
- P27709 · AlphaFold monomer V2.0 prediction for DNA-binding transcriptional activator hetr (P27709) · a predicted model of the same protein · chain B against A, TM-score 0.97
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 P27709
- Elsewhere: RCSB PDB 4YRV · PDBe 4YRV · UniProt P27709
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.