Research workbench
Crystal structure of a stabilized pan ene bimolecular triplex with a gc-clamped polya tail, in complex with Fab-bl-3,6.
Analyse Crystal structure of a stabilized pan ene bimolecular triplex with a gc-clamped… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6X5M
- Type
- protein + RNA
- Length
- 982 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Light chain Fab bl-3 6; Heavy chain Fab bl-3 6; Ggpan RNA (39-mer); GGCA9 RNA (12-mer)
- Ligands
- SO4
- Pockets
- 15 · best druggability 0.70
Structure
x-ray diffraction · 4 distinct chains · 6% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| l, L | Light chain Fab bl-3 6 | protein | 215 | 4% helix, 48% strand | — |
| h, H | Heavy chain Fab bl-3 6 | protein | 225 | 8% helix, 50% strand | — |
| R, r | Ggpan RNA (39-mer) | rna | 39 | — | — |
| A, a | GGCA9 RNA (12-mer) | rna | 12 | — | — |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 2 copies · chains l, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 56 | 0.70 | 0.97 | 24 | empty |
| 2 | 70 | 0.66 | 0.93 | 16 | empty |
| 3 | 417 | 0.62 | 0.78 | 40 | empty |
| 4 | 555 | 0.61 | 0.74 | 61 | empty |
| 5 | 376 | 0.58 | 0.76 | 30 | empty |
Interfaces
9 interfaces between chains.
- H–L · 1943 Ų buried · 9 hydrogen bonds · protein-protein
- l–h · 1897 Ų buried · 13 hydrogen bonds · protein-protein
- R–A · 1169 Ų buried · 84 hydrogen bonds · nucleic-nucleic
- r–a · 1103 Ų buried · 90 hydrogen bonds · nucleic-nucleic
- H–R · 669 Ų buried · 21 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 6X5M · Crystal structure of a stabilized PAN ENE bimolecular triplex with a GC-clamped polyA… · the same entry in another collection · chain l against l, 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
- Elsewhere: RCSB PDB 6X5M · PDBe 6X5M
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