Research workbench
Ternary complex of tert (telomerase reverse transcriptase) with RNA template, DNA primer, an incoming dgtp and a downstream hybrid duplex
Analyse Ternary complex of tert (telomerase reverse transcriptase) with RNA template… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7KQN
- Type
- protein + DNA + RNA
- Length
- 1,256 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Telomerase reverse transcriptase; RNA (5'- R(*CP*AP*AP*AP*GP*AP*AP*AP*UP*CP*CP*AP*GP*GP*UP…
- EC
- 2.7.7.49
- UniProt
- Q0QHL8
- Ligands
- DGT, CA
- Pockets
- 16 · best druggability 0.84
Structure
x-ray diffraction · 4 distinct chains · 49% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Telomerase reverse transcriptase (EC 2.7.7.49) | protein | 596 | 49% helix, 13% strand | Q0QHL8 |
| B, E | RNA (5'- R(*CP*AP*AP*AP*GP*AP*AP*AP*UP*CP*CP*AP*GP*GP*UP*GP*CP*A)-3') | rna | 18 | — | — |
| C, F | DNA (5'-D(*GP*CP*AP*CP*CP*TP*G)-3') | dna | 7 | — | — |
| I, J | DNA (5'-D(*TP*TP*CP*TP*TP*TP*G)-3') | dna | 7 | — | — |
Ligands and binding sites
- DGT · 2'-deoxyguanosine-5'-triphosphate · ligand · 2 copies · chains A, B, C, D, E, F
- CA · Calcium ion · metal · 2 copies · chains A, D, F
- EDO · 1,2-ethanediol · additive · 21 copies · chains A, D, E
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · 2 copies · chains A
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 964 | 0.84 | 0.85 | 96 | CA, DGT |
| 2 | 935 | 0.84 | 0.85 | 102 | EDO, CA, DGT |
| 3 | 919 | 0.83 | 0.85 | 76 | EDO, PEG |
| 4 | 100 | 0.77 | 0.98 | 20 | empty |
| 5 | 706 | 0.75 | 0.81 | 61 | empty |
Interfaces
17 interfaces between chains.
- D–E · 1266 Ų buried · 13 hydrogen bonds · protein-nucleic
- A–B · 1255 Ų buried · 16 hydrogen bonds · protein-nucleic
- D–F · 656 Ų buried · 11 hydrogen bonds · protein-nucleic
- A–C · 624 Ų buried · 11 hydrogen bonds · protein-nucleic
- A–D · 456 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 7KQN · Ternary complex of TERT (telomerase reverse transcriptase) with RNA template, DNA primer… · the same entry in another collection · chain E against E, 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 Q0QHL8
- Elsewhere: RCSB PDB 7KQN · PDBe 7KQN · UniProt Q0QHL8
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