Research workbench
Human endogenous retrovirus (herv-K) reverse transcriptase ternary complex with dsdna template primer and dntp
Analyse Human endogenous retrovirus (herv-K) reverse transcriptase ternary complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7SR6
- Type
- protein + DNA
- Length
- 2,082 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Polymerase; DNA (5'- D(P*GP*GP*GP*AP*CP*CP*TP*GP*AP*AP*AP*GP*CP*GP*AP*AP*AP*GP*GP*GP*AP*AP…
- UniProt
- V9H0F6
- Ligands
- DCP, TTP, K, MG, CL
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 6 distinct chains · 38% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, F | Polymerase | protein | 566 | 36% helix, 21% strand | V9H0F6 |
| B, G | Polymerase | protein | 432 | 40% helix, 18% strand | V9H0F6 |
| D | DNA (5'- D(P*GP*GP*GP*AP*CP*CP*TP*GP*AP*AP*AP*GP*CP*GP*AP*AP*AP*GP*GP*GP*AP*AP *a)-3') | dna | 23 | — | — |
| E | DNA (5'- D(P*TP*TP*TP*CP*CP*CP*TP*TP*TP*CP*GP*CP*TP*TP*TP*CP*AP*GP*GP*T)-3') | dna | 20 | — | — |
| H | DNA (5'- D(P*GP*GP*GP*AP*CP*CP*TP*GP*AP*AP*AP*GP*CP*GP*AP*AP*AP*GP*GP*GP*AP*AP *a)-3') | dna | 23 | — | — |
| I | DNA (5'- D(P*TP*TP*TP*CP*CP*CP*TP*TP*TP*CP*GP*CP*TP*TP*TP*CP*AP*GP*GP*T)-3') | dna | 20 | — | — |
Ligands and binding sites
- DCP · 2'-deoxycytidine-5'-triphosphate · ligand · chains A, D, E
- TTP · Thymidine-5'-triphosphate · ligand · chains F, H, I
- K · Potassium ion · metal · 11 copies · chains A, E, B, D, F, H, G
- MG · Magnesium ion · metal · 5 copies · chains A, D, F, G
- CL · Chloride ion · ion · 2 copies · chains F, G
- DIO · 1,4-diethylene dioxide · additive · 34 copies · chains A, B, F, G, H
- EDO · 1,2-ethanediol · additive · 7 copies · chains A, B, F, G
- PG6 · 1-(2-methoxy-ethoxy)-2-{2-[2-(2-methoxy-ethoxy]-ethoxy}-ethane · additive · 2 copies · chains B, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
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 | 537 | 0.83 | 0.89 | 63 | DIO |
| 2 | 508 | 0.83 | 0.89 | 63 | empty |
| 3 | 970 | 0.81 | 0.83 | 78 | DIO |
| 4 | 823 | 0.78 | 0.81 | 97 | DIO, K |
| 5 | 636 | 0.76 | 0.82 | 87 | DIO |
Interfaces
17 interfaces between chains.
- F–G · 2274 Ų buried · 27 hydrogen bonds · protein-protein
- A–B · 2235 Ų buried · 23 hydrogen bonds · protein-protein
- F–H · 1128 Ų buried · 8 hydrogen bonds · protein-nucleic
- A–D · 1007 Ų buried · 9 hydrogen bonds · protein-nucleic
- H–I · 912 Ų buried · 85 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 7SR6 · Human Endogenous Retrovirus (HERV-K) reverse transcriptase ternary complex with dsDNA… · 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 V9H0F6
- Elsewhere: RCSB PDB 7SR6 · PDBe 7SR6 · UniProt V9H0F6
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