MolNFT v1 · #10128 · protein + DNA
Integration host FACTOR/DNA complex
1IHF · DNA (35-mer): “Integration host FACTOR/DNA complex”. X-ray diffraction, 1 ligand (CD), 4 pockets (best druggability 0.81). MolNFT v1 #10128 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1IHF
- Type
- protein + DNA
- Length
- 260 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (35-mer); DNA (5'-D(*GP*GP*CP*CP*AP*AP*AP*AP*AP*AP*GP*CP*AP*TP*T)- 3'); DNA (5'…
- UniProt
- P0A6X7, P0A6Y1
- Ligands
- CD
- Pockets
- 4 · best druggability 0.81
Structure
x-ray diffraction · 5 distinct chains · 41% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | DNA (35-mer) | dna | 35 | — | — |
| D | DNA (5'-D(*GP*GP*CP*CP*AP*AP*AP*AP*AP*AP*GP*CP*AP*TP*T)- 3') | dna | 15 | — | — |
| E | DNA (5'- D(*GP*CP*TP*TP*AP*TP*CP*AP*AP*TP*TP*TP*GP*TP*TP*GP*C P*AP*CP*C)-3') | dna | 20 | — | — |
| A | Protein (integration host factor (alpha) (ihf)) | protein | 96 | 42% helix, 29% strand | P0A6X7 |
| B | Protein (integration host factor (beta) (ihf)) | protein | 94 | 40% helix, 30% strand | P0A6Y1 |
Ligands and binding sites
- CD · Cadmium ion · metal · 15 copies · chains C, B, D, E, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1005 | 0.81 | 0.82 | 94 | CD |
| 2 | 345 | 0.56 | 0.75 | 32 | CD |
| 3 | 164 | 0.45 | 0.75 | 18 | CD |
| 4 | 92 | 0.35 | 0.75 | 15 | empty |
Interfaces
10 interfaces between chains.
- A–B · 2504 Ų buried · 29 hydrogen bonds · protein-protein
- C–E · 941 Ų buried · 75 hydrogen bonds · nucleic-nucleic
- C–B · 789 Ų buried · 16 hydrogen bonds · protein-nucleic
- C–D · 698 Ų buried · 46 hydrogen bonds · nucleic-nucleic
- C–A · 687 Ų buried · 10 hydrogen bonds · protein-nucleic
Compared structures
- 1IHF · Integration host FACTOR/DNA complex · the same entry in another collection · chain D against D, TM-score 1.00
- P0A6Y1 · AlphaFold monomer V2.0 prediction for integration host factor subunit beta (P0A6Y1) · a predicted model of the same protein · chain B against A, TM-score 0.99
- P0A6X7 · AlphaFold monomer V2.0 prediction for integration host factor subunit alpha (P0A6X7) · a predicted model of the same protein · chain A against A, TM-score 0.96
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 P0A6X7
- Every structure of UniProt P0A6Y1
- Elsewhere: RCSB PDB 1IHF · PDBe 1IHF · UniProt P0A6X7 · UniProt P0A6Y1
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