Research workbench
Structure of fitab bound to IR36 DNA fragment
Analyse Structure of fitab bound to IR36 DNA fragment in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2H1O
- Type
- protein + DNA
- Length
- 900 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- IR36-strand 1; IR36-strand 2; Trafficking protein B; Trafficking protein a
- UniProt
- Q9RF91, Q9RF92
- Pockets
- 11 · best druggability 0.58
Structure
x-ray diffraction · 8 distinct chains · 58% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| U | IR36-strand 1 | dna | 36 | — | — |
| V | IR36-strand 2 | dna | 36 | — | — |
| A, C | Trafficking protein B | protein | 143 | 58% helix, 10% strand | Q9RF91 |
| B, D | Trafficking protein B | protein | 140 | 55% helix, 11% strand | Q9RF91 |
| E | Trafficking protein a | protein | 68 | 59% helix, 4% strand | Q9RF92 |
| F | Trafficking protein a | protein | 64 | 61% helix, 5% strand | Q9RF92 |
| G | Trafficking protein a | protein | 67 | 61% helix, 4% strand | Q9RF92 |
| H | Trafficking protein a | protein | 63 | 60% helix, 5% strand | Q9RF92 |
Pockets
11 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 374 | 0.58 | 0.76 | 31 | empty |
| 2 | 388 | 0.58 | 0.76 | 48 | empty |
| 3 | 169 | 0.51 | 0.78 | 25 | empty |
| 4 | 144 | 0.48 | 0.78 | 21 | empty |
| 5 | 96 | 0.43 | 0.79 | 24 | empty |
Interfaces
23 interfaces between chains.
- U–V · 1555 Ų buried · 133 hydrogen bonds · nucleic-nucleic
- F–G · 1441 Ų buried · 32 hydrogen bonds · protein-protein
- E–H · 1425 Ų buried · 26 hydrogen bonds · protein-protein
- A–E · 1376 Ų buried · 25 hydrogen bonds · protein-protein
- C–G · 1356 Ų buried · 23 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (nucleotide modification).
Compared structures
- 2H1O · Structure of FitAB bound to IR36 DNA fragment · the same entry in another collection · chain U against U, 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 Q9RF91
- Every structure of UniProt Q9RF92
- Elsewhere: RCSB PDB 2H1O · PDBe 2H1O · UniProt Q9RF91 · UniProt Q9RF92
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