Research workbench
Crystal structure of MSL5 protein in complex with RNA at 1.8 a
Analyse Crystal structure of MSL5 protein in complex with RNA at 1.8 a in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4WAN
- Type
- protein + RNA
- Length
- 517 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Branchpoint-bridging protein; RNA (5'-R(P*UP*AP*CP*UP*AP*AP*CP*A)-3')
- UniProt
- Q12186
- Ligands
- SO4
- Pockets
- 5 · best druggability 0.76
Structure
x-ray diffraction · 6 distinct chains · 44% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Branchpoint-bridging protein | protein | 124 | 44% helix, 15% strand | Q12186 |
| B, H | RNA (5'-R(P*UP*AP*CP*UP*AP*AP*CP*A)-3') | rna | 7 | — | — |
| C | Branchpoint-bridging protein | protein | 125 | 43% helix, 15% strand | Q12186 |
| D, F | RNA (5'-R(P*UP*AP*CP*UP*AP*AP*CP*A)-3') | rna | 8 | — | — |
| E | Branchpoint-bridging protein | protein | 122 | 42% helix, 14% strand | Q12186 |
| G | Branchpoint-bridging protein | protein | 116 | 46% helix, 15% strand | Q12186 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 4 copies · chains A, B, G
- GOL · Glycerol · additive · 5 copies · chains A, C, E
- ACT · Acetate ion · additive · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 934 | 0.76 | 0.79 | 93 | empty |
| 2 | 66 | 0.72 | 0.97 | 16 | empty |
| 3 | 89 | 0.45 | 0.80 | 15 | empty |
| 4 | 70 | 0.43 | 0.80 | 15 | empty |
| 5 | 83 | 0.38 | 0.77 | 17 | empty |
Interfaces
12 interfaces between chains.
- A–B · 1107 Ų buried · 25 hydrogen bonds · protein-nucleic
- G–H · 1088 Ų buried · 28 hydrogen bonds · protein-nucleic
- C–D · 1062 Ų buried · 22 hydrogen bonds · protein-nucleic
- E–F · 1058 Ų buried · 26 hydrogen bonds · protein-nucleic
- C–E · 802 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 4WAN · Crystal structure of Msl5 protein in complex with RNA at 1.8 A · the same entry in another collection · chain H against H, TM-score 1.00
- Q12186 · AlphaFold monomer V2.0 prediction for branchpoint-bridging protein (Q12186) · a predicted model of the same protein · chain C against A, TM-score 0.98
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 Q12186
- Elsewhere: RCSB PDB 4WAN · PDBe 4WAN · UniProt Q12186
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