Research workbench
Gsi-iic rt template-switching complex (twinned)
Analyse Gsi-iic rt template-switching complex (twinned) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7K9Y
- Type
- protein + DNA + RNA
- Length
- 893 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Trt; DNA (5'-D(*CP*TP*CP*CP*AP*GP*GP*CP*AP*AP*C)-3'); RNA…
- UniProt
- E2GM63
- Ligands
- DTP, MG, SO4
- Pockets
- 7 · best druggability 0.81
Structure
x-ray diffraction · 5 distinct chains · 54% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Trt | protein | 425 | 55% helix, 11% strand | E2GM63 |
| B, E | DNA (5'-D(*CP*TP*CP*CP*AP*GP*GP*CP*AP*AP*C)-3') | dna | 11 | — | — |
| C, F | RNA (5'-R(*UP*UP*GP*CP*CP*UP*GP*GP*AP*G)-3') | rna | 10 | — | — |
| D | Trt | protein | 418 | 54% helix, 11% strand | E2GM63 |
| G, H | RNA (5'-R(*U*UP*UP*UP*G)-3') | rna | 4 | — | — |
Ligands and binding sites
- DTP · 2'-deoxyadenosine 5'-triphosphate · ligand · 2 copies · chains A, B, G, D, E, H
- MG · Magnesium ion · metal · 2 copies · chains A, D
- SO4 · Sulfate ion · ion · 3 copies · chains A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 921 | 0.81 | 0.83 | 81 | DTP, MG |
| 2 | 1111 | 0.78 | 0.80 | 74 | DTP, MG |
| 3 | 348 | 0.72 | 0.85 | 47 | SO4 |
| 4 | 260 | 0.57 | 0.79 | 21 | empty |
| 5 | 83 | 0.48 | 0.82 | 22 | empty |
Interfaces
14 interfaces between chains.
- A–D · 1293 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 687 Ų buried · 6 hydrogen bonds · protein-nucleic
- D–E · 617 Ų buried · 4 hydrogen bonds · protein-nucleic
- D–H · 488 Ų buried · 7 hydrogen bonds · protein-nucleic
- E–F · 488 Ų buried · 32 hydrogen bonds · nucleic-nucleic
Compared structures
- 7K9Y · GsI-IIC RT Template-Switching Complex (twinned) · the same entry in another collection · chain A against A, 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 E2GM63
- Elsewhere: RCSB PDB 7K9Y · PDBe 7K9Y · UniProt E2GM63
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