MolNFT v1 · #173874 · protein
Human BRR2 helicase region in complex with C-tail deleted JAB1 and mant-ADP
7BDL · U5 small nuclear ribonucleoprotein 200 kda helicase: “Human BRR2 helicase region in complex with C-tail deleted JAB1 and mant-ADP”. X-ray diffraction, 2 ligands (TG8, MG), 20 pockets (best druggability 0.84). MolNFT v1 #173874 on…
- PDB
- 7BDL
- Type
- protein
- Length
- 1,987 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- U5 small nuclear ribonucleoprotein 200 kda helicase; Pre-mRNA-processing-splicing factor 8
- EC
- 3.6.4.13
- UniProt
- O75643, Q6P2Q9
- Ligands
- TG8, MG
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | U5 small nuclear ribonucleoprotein 200 kda helicase (EC 3.6.4.13) | protein | 1725 | 42% helix, 17% strand | O75643 |
| J | Pre-mRNA-processing-splicing factor 8 | protein | 262 | 21% helix, 26% strand | Q6P2Q9 |
Ligands and binding sites
- TG8 · [(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-4-oxidanyl-2-[[oxidanyl(phosphonooxy) phosphoryl]oxymethyl]oxolan-3-yl] 2-(methylamino) benzoate · ligand · 2 copies · chains B
- MG · Magnesium ion · metal · 2 copies · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 752 | 0.84 | 0.87 | 79 | empty |
| 2 | 977 | 0.80 | 0.82 | 78 | empty |
| 3 | 785 | 0.77 | 0.81 | 72 | empty |
| 4 | 890 | 0.75 | 0.78 | 61 | TG8, MG |
| 5 | 255 | 0.73 | 0.87 | 36 | empty |
Interfaces
1 interface between chains.
- B–J · 1773 Ų buried · 19 hydrogen bonds · protein-protein
Compared structures
- 7BDL · Human Brr2 Helicase Region in complex with C-tail deleted Jab1 and mant-ADP · the same entry in another collection · chain B against B, 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 O75643
- Every structure of UniProt Q6P2Q9
- Elsewhere: RCSB PDB 7BDL · PDBe 7BDL · UniProt O75643 · UniProt Q6P2Q9
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