Research workbench
Cryo-EM structure of TY3 retrotransposon targeting a tfiiib-bound tRNA gene
Analyse Cryo-EM structure of TY3 retrotransposon targeting a tfiiib-bound tRNA gene in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7Q5B
- Type
- protein + DNA
- Length
- 2,423 residues
- Chains
- 13
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (56-mer); DNA (31-mer); DNA (34-mer); DNA (9-mer); Transposon TY3-G gag-pol…
- UniProt
- Q99315, P46678, P13393, P29056
- Pockets
- 20 · best druggability 0.87
Structure
electron microscopy · 12 distinct chains · 36% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| R | DNA (56-mer) | dna | 56 | — | — |
| S | DNA (31-mer) | dna | 31 | — | — |
| r | DNA (34-mer) | dna | 34 | — | — |
| s | DNA (9-mer) | dna | 9 | — | — |
| A | Transposon TY3-G gag-pol polyprotein | protein | 418 | 34% helix, 11% strand | Q99315 |
| B | Transposon TY3-G gag-pol polyprotein | protein | 482 | 33% helix, 12% strand | Q99315 |
| C | Transposon TY3-G gag-pol polyprotein | protein | 482 | 28% helix, 11% strand | Q99315 |
| D | Transposon TY3-G gag-pol polyprotein | protein | 334 | 37% helix, 10% strand | Q99315 |
| X | Transcription factor tfiiib component B'' | protein | 70 | 73% helix, 0% strand | P46678 |
| Y | Tata-box-binding protein | protein | 180 | 25% helix, 31% strand | P13393 |
| Z | Transcription factor iiib 70 kda subunit | protein | 289 | 55% helix, 0% strand | P29056 |
| t, u | DNA (19-mer) | dna | 19 | — | — |
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 891 | 0.87 | 0.89 | 93 | empty |
| 2 | 757 | 0.86 | 0.90 | 93 | empty |
| 3 | 815 | 0.84 | 0.87 | 76 | empty |
| 4 | 785 | 0.79 | 0.82 | 75 | empty |
| 5 | 711 | 0.79 | 0.84 | 69 | empty |
Interfaces
39 interfaces between chains.
- Y–Z · 3154 Ų buried · 25 hydrogen bonds · protein-protein
- A–C · 3100 Ų buried · 18 hydrogen bonds · protein-protein
- B–D · 2982 Ų buried · 23 hydrogen bonds · protein-protein
- A–B · 2498 Ų buried · 22 hydrogen bonds · protein-protein
- R–r · 1452 Ų buried · 91 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 7Q5B · Cryo-EM structure of Ty3 retrotransposon targeting a TFIIIB-bound tRNA gene · the same entry in another collection · chain u against u, 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 Q99315
- Every structure of UniProt P46678
- Every structure of UniProt P13393
- Every structure of UniProt P29056
- Elsewhere: RCSB PDB 7Q5B · PDBe 7Q5B · UniProt Q99315 · UniProt P46678 · UniProt P13393 · UniProt P29056
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