Research workbench
Crystal structure of an irf-2/DNA complex.
Analyse Crystal structure of an irf-2/DNA complex. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2IRF
- Type
- protein + DNA
- Length
- 728 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (5'-D(P*AP*AP*GP*TP*GP*AP*AP*AP*GP*(5IU) P*GP*A)-3'); DNA (5'…
- UniProt
- P23906
- Ligands
- K
- Pockets
- 12 · best druggability 0.70
Structure
x-ray diffraction · 4 distinct chains · 34% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | DNA (5'-D(P*AP*AP*GP*TP*GP*AP*AP*AP*GP*(5IU) P*GP*A)-3') | dna | 12 | — | — |
| D, F | DNA (5'- D(*TP*TP*CP*AP*CP*TP*TP*TP*CP*AP*CP*(5IU)P*T)-3') | dna | 13 | — | — |
| E | DNA (5'- D(*TP*TP*CP*AP*CP*TP*TP*TP*CP*AP*CP*(5IU)P*T)-3') | dna | 12 | — | — |
| G, H, I, J, K, L | Interferon regulatory factor 2 | protein | 109 | 34% helix, 17% strand | P23906 |
Ligands and binding sites
- K · Potassium ion · metal · 6 copies · chains G, H, I, J, K, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 704 | 0.70 | 0.78 | 57 | empty |
| 2 | 474 | 0.63 | 0.77 | 59 | empty |
| 3 | 346 | 0.59 | 0.77 | 34 | empty |
| 4 | 302 | 0.57 | 0.78 | 32 | empty |
| 5 | 196 | 0.48 | 0.76 | 19 | empty |
Interfaces
31 interfaces between chains.
- B–E · 560 Ų buried · 50 hydrogen bonds · nucleic-nucleic
- C–D · 554 Ų buried · 50 hydrogen bonds · nucleic-nucleic
- A–F · 552 Ų buried · 50 hydrogen bonds · nucleic-nucleic
- B–J · 445 Ų buried · 14 hydrogen bonds · protein-nucleic
- C–L · 440 Ų buried · 11 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 6 modified (nucleotide modification).
Compared structures
- 2IRF · Crystal structure of an irf-2/DNA complex. · the same entry in another collection · chain L against L, TM-score 1.00
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 P23906
- Elsewhere: RCSB PDB 2IRF · PDBe 2IRF · UniProt P23906
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