Research workbench
Human BRR2 helicase region in complex with C-tail deleted JAB1 and mant-atpgammas
Analyse Human BRR2 helicase region in complex with C-tail deleted JAB1 and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7BDJ
- Type
- protein
- Length
- 1,984 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
- TGB, MG
- Pockets
- 20 · best druggability 0.85
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 | 1722 | 41% helix, 17% strand | O75643 |
| J | Pre-mRNA-processing-splicing factor 8 | protein | 262 | 25% helix, 25% strand | Q6P2Q9 |
Ligands and binding sites
- TGB · [[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3-[2-(methylamino)phenyl]carbonyloxy-4-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-sulfanyl-phosphinic acid · 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, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1135 | 0.85 | 0.85 | 93 | empty |
| 2 | 1126 | 0.79 | 0.81 | 113 | empty |
| 3 | 545 | 0.77 | 0.84 | 69 | empty |
| 4 | 670 | 0.75 | 0.81 | 70 | empty |
| 5 | 439 | 0.74 | 0.84 | 59 | TGB, MG |
Interfaces
1 interface between chains.
- B–J · 1798 Ų buried · 20 hydrogen bonds · protein-protein
Compared structures
- 7BDJ · Human Brr2 Helicase Region in complex with C-tail deleted Jab1 and mant-ATPgammaS · 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 7BDJ · PDBe 7BDJ · UniProt O75643 · UniProt Q6P2Q9
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