Research workbench
Crystal structure of the heterodimeric hif-1A:ARNT complex with hre DNA
Analyse Crystal structure of the heterodimeric hif-1A:ARNT complex with hre DNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4ZPR
- Type
- protein + DNA
- Length
- 556 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Aryl hydrocarbon receptor nuclear translocator; Hypoxia-inducible factor 1-alpha; DNA…
- UniProt
- P53762, Q61221
- Pockets
- 12 · best druggability 0.78
Structure
x-ray diffraction · 4 distinct chains · 34% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Aryl hydrocarbon receptor nuclear translocator | protein | 235 | 38% helix, 23% strand | P53762 |
| B | Hypoxia-inducible factor 1-alpha | protein | 279 | 30% helix, 24% strand | Q61221 |
| C | DNA (5'- D(*GP*GP*CP*TP*GP*CP*GP*TP*AP*CP*GP*TP*GP*CP*GP*GP*GP*TP*CP*GP*T)- 3') | dna | 21 | — | — |
| D | DNA (5'- D(*CP*AP*CP*GP*AP*CP*CP*CP*GP*CP*AP*CP*GP*TP*AP*CP*GP*CP*AP*GP*C)- 3') | dna | 21 | — | — |
Pockets
12 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 483 | 0.78 | 0.86 | 51 | empty |
| 2 | 86 | 0.75 | 0.96 | 21 | empty |
| 3 | 661 | 0.70 | 0.78 | 70 | empty |
| 4 | 161 | 0.65 | 0.86 | 21 | empty |
| 5 | 217 | 0.58 | 0.79 | 33 | empty |
Interfaces
6 interfaces between chains.
- A–B · 3111 Ų buried · 21 hydrogen bonds · protein-protein
- C–D · 896 Ų buried · 81 hydrogen bonds · nucleic-nucleic
- B–D · 474 Ų buried · 9 hydrogen bonds · protein-nucleic
- A–C · 454 Ų buried · 6 hydrogen bonds · protein-nucleic
- B–C · 326 Ų buried · 6 hydrogen bonds · protein-nucleic
Compared structures
- 4ZPR · Crystal Structure of the Heterodimeric HIF-1a:ARNT Complex with HRE DNA · the same entry in another collection · chain A against A, TM-score 1.00
- Q61221 · AlphaFold monomer V2.0 prediction for hypoxia-inducible factor 1-alpha (Q61221) · a predicted model of the same protein · chain B against A, TM-score 0.97
- P53762 · AlphaFold monomer V2.0 prediction for aryl hydrocarbon receptor nuclear translocator… · a predicted model of the same protein · chain A against A, TM-score 0.77
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 P53762
- Every structure of UniProt Q61221
- Elsewhere: RCSB PDB 4ZPR · PDBe 4ZPR · UniProt P53762 · UniProt Q61221
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