Research workbench
Structures of HIV-1 rt and RNA-DNA complex reveal a unique rt conformation and substrate interface
Analyse Structures of HIV-1 rt and RNA-DNA complex reveal a unique rt conformation and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4B3P
- Type
- protein + DNA + RNA
- Length
- 965 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Reverse TRANSCRIPTASE/RIBONUCLEASE H; P51 rt; DNA; RNA
- EC
- 2.7.7.49, 2.7.7.7, 3.1.26.13, 3.4.23.16, 3.1.13.2
- UniProt
- P04585
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 4 distinct chains · 33% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Reverse TRANSCRIPTASE/RIBONUCLEASE H (EC 2.7.7.49, 2.7.7.7, 3.1.26.13, 3.4.23.16, 3.1.13.2) | protein | 519 | 30% helix, 21% strand | P04585 |
| B | P51 rt (EC 2.7.7.49, 2.7.7.7, 3.1.26.13, 3.4.23.16) | protein | 404 | 36% helix, 18% strand | P04585 |
| D | DNA | dna | 21 | — | — |
| R | RNA | rna | 21 | — | — |
Pockets
20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1073 | 0.86 | 0.87 | 104 | empty |
| 2 | 903 | 0.82 | 0.84 | 75 | empty |
| 3 | 815 | 0.78 | 0.81 | 73 | empty |
| 4 | 241 | 0.70 | 0.85 | 33 | empty |
| 5 | 644 | 0.69 | 0.77 | 67 | empty |
Interfaces
6 interfaces between chains.
- A–B · 2620 Ų buried · 22 hydrogen bonds · protein-protein
- D–R · 986 Ų buried · 90 hydrogen bonds · nucleic-nucleic
- A–D · 738 Ų buried · 7 hydrogen bonds · protein-nucleic
- A–R · 675 Ų buried · 5 hydrogen bonds · protein-nucleic
- B–D · 131 Ų buried · 0 hydrogen bonds · protein-nucleic
Compared structures
- 4B3P · Structures of HIV-1 RT and RNA-DNA Complex Reveal a Unique RT Conformation and Substrate… · 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 P04585
- Elsewhere: RCSB PDB 4B3P · PDBe 4B3P · UniProt P04585
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