Research workbench
+3 extended HIV-1 reverse transcriptase initiation complex core (displaced state)
Analyse +3 extended HIV-1 reverse transcriptase initiation complex core (displaced… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6WB2
- Type
- protein + RNA
- Length
- 1,021 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HIV-1 viral RNA genome fragment; TRNA lysine 3; Reverse TRANSCRIPTASE/RIBONUCLEASE H…
- EC
- 2.7.7.49, 2.7.7.7, 3.1.26.13
- UniProt
- P03366
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · 4 distinct chains · 33% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | HIV-1 viral RNA genome fragment | rna | 33 | — | — |
| D | TRNA lysine 3 | rna | 42 | — | — |
| A | Reverse TRANSCRIPTASE/RIBONUCLEASE H (EC 2.7.7.49, 2.7.7.7, 3.1.26.13) | protein | 540 | 31% helix, 18% strand | P03366 |
| B | Reverse transcriptase P51 subunit | protein | 406 | 34% helix, 16% strand | P03366 |
Pockets
20 pockets found on a 1 Å grid, 19 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 876 | 0.85 | 0.86 | 112 | empty |
| 2 | 650 | 0.77 | 0.83 | 74 | empty |
| 3 | 545 | 0.75 | 0.82 | 53 | empty |
| 4 | 612 | 0.73 | 0.80 | 71 | empty |
| 5 | 159 | 0.73 | 0.91 | 36 | empty |
Interfaces
6 interfaces between chains.
- A–B · 2267 Ų buried · 11 hydrogen bonds · protein-protein
- C–D · 1294 Ų buried · 95 hydrogen bonds · nucleic-nucleic
- C–A · 815 Ų buried · 10 hydrogen bonds · protein-nucleic
- D–A · 417 Ų buried · 3 hydrogen bonds · protein-nucleic
- D–B · 64 Ų buried · 0 hydrogen bonds · protein-nucleic
Compared structures
- 6WB2 · +3 extended HIV-1 reverse transcriptase initiation complex core (displaced state) · the same entry in another collection · chain C against C, 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 P03366
- Elsewhere: RCSB PDB 6WB2 · PDBe 6WB2 · UniProt P03366
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