MolNFT v1 · #40186 · protein + DNA
Single chain integration host factor protein (SCIHF2) in complex with DNA
2IIE · Phage P H' site: “Single chain integration host factor protein (SCIHF2) in complex with DNA”. X-ray diffraction, 1 ligand (MN), 5 pockets (best druggability 0.78). MolNFT v1 #40186 on GenesisL1: 3D structure, binding sites and…
- PDB
- 2IIE
- Type
- protein + DNA
- Length
- 274 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phage P H' site; DNA (5'- D(*DGP*DGP*DCP*DCP*DAP*DAP*DAP*DAP*DAP*DAP*DGP*DCP*DAP*DTP*DT)-3…
- UniProt
- P0A6X7, P0A6Y1
- Ligands
- MN
- Pockets
- 5 · best druggability 0.78
Structure
x-ray diffraction · 4 distinct chains · 38% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | Phage P H' site | dna | 35 | — | — |
| D | DNA (5'- D(*DGP*DGP*DCP*DCP*DAP*DAP*DAP*DAP*DAP*DAP*DGP*DCP*DAP*DTP*DT)-3') | dna | 15 | — | — |
| E | DNA (5'- D(*DGP*DCP*DTP*DTP*DAP*DTP*DCP*DAP*DAP*DTP*DTP*DTP*DGP*DTP*DTP*DGP*DC P*DAP*DCP*DC)-3') | dna | 20 | — | — |
| A | Integration host factor | protein | 204 | 38% helix, 27% strand | P0A6X7, P0A6Y1 |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 7 copies · chains C, D, E, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 812 | 0.78 | 0.82 | 67 | empty |
| 2 | 350 | 0.66 | 0.81 | 32 | empty |
| 3 | 379 | 0.60 | 0.77 | 40 | MN |
| 4 | 149 | 0.41 | 0.74 | 16 | empty |
| 5 | 112 | 0.39 | 0.75 | 20 | empty |
Interfaces
6 interfaces between chains.
- C–A · 1436 Ų buried · 27 hydrogen bonds · protein-nucleic
- C–E · 929 Ų buried · 77 hydrogen bonds · nucleic-nucleic
- E–A · 926 Ų buried · 25 hydrogen bonds · protein-nucleic
- C–D · 686 Ų buried · 55 hydrogen bonds · nucleic-nucleic
- D–A · 303 Ų buried · 7 hydrogen bonds · protein-nucleic
Compared structures
- 2IIE · single chain Integration Host Factor protein (scIHF2) in complex with DNA · the same entry in another collection · chain C against C, TM-score 1.00
- 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 0.47
- P0A6Y1 · AlphaFold monomer V2.0 prediction for integration host factor subunit beta (P0A6Y1) · a predicted model of the same protein · chain A against A, TM-score 0.45
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 2IIE · PDBe 2IIE · UniProt P0A6X7 · UniProt P0A6Y1
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