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Crystal structure of AFT2 in complex with DNA
Analyse Crystal structure of AFT2 in complex with DNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4LMG
- Type
- protein + DNA
- Length
- 533 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Iron-regulated transcriptional activator AFT2…
- UniProt
- Q08957
- Ligands
- ZN
- Pockets
- 10 · best druggability 0.69
Structure
x-ray diffraction · 6 distinct chains · 37% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Iron-regulated transcriptional activator AFT2 | protein | 120 | 38% helix, 24% strand | Q08957 |
| B, C | Iron-regulated transcriptional activator AFT2 | protein | 121 | 36% helix, 23% strand | Q08957 |
| D | Iron-regulated transcriptional activator AFT2 | protein | 120 | 38% helix, 24% strand | Q08957 |
| E, G | 5'-D(*TP*AP*AP*TP*GP*GP*GP*TP*GP*CP*AP*CP*T)-3' | dna | 13 | — | — |
| F | 5'-D(*AP*AP*GP*TP*GP*CP*AP*CP*CP*CP*AP*TP*T)-3' | dna | 12 | — | — |
| H | 5'-D(*AP*AP*GP*TP*GP*CP*AP*CP*CP*CP*AP*TP*T)-3' | dna | 13 | — | — |
Ligands and binding sites
- ZN · Zinc ion · metal · 6 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 837 | 0.69 | 0.76 | 69 | empty |
| 2 | 581 | 0.68 | 0.78 | 79 | empty |
| 3 | 502 | 0.67 | 0.78 | 52 | empty |
| 4 | 177 | 0.42 | 0.74 | 28 | empty |
| 5 | 96 | 0.39 | 0.76 | 14 | empty |
Interfaces
14 interfaces between chains.
- E–F · 566 Ų buried · 52 hydrogen bonds · nucleic-nucleic
- G–H · 563 Ų buried · 47 hydrogen bonds · nucleic-nucleic
- C–F · 447 Ų buried · 11 hydrogen bonds · protein-nucleic
- C–E · 440 Ų buried · 8 hydrogen bonds · protein-nucleic
- D–H · 438 Ų buried · 11 hydrogen bonds · protein-nucleic
Compared structures
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 Q08957
- Elsewhere: RCSB PDB 4LMG · PDBe 4LMG · UniProt Q08957
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