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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
- 4B3O
- Type
- protein + DNA + RNA
- Length
- 996 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Reverse TRANSCRIPTASE/RIBONUCLEASE H; P51 rt; 5'-D(*CP*GP*TP*AP*TP*GP*CP*CP*TP*AP*TP*AP*GP…
- EC
- 2.7.7.49, 2.7.7.7, 3.1.26.13, 3.4.23.16, 3.1.13.2
- UniProt
- P04585
- Ligands
- EFZ, CA
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 4 distinct chains · 32% 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 | 540 | 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 | 410 | 35% helix, 19% strand | P04585 |
| D | 5'-D(*CP*GP*TP*AP*TP*GP*CP*CP*TP*AP*TP*AP*GP*TP *TP*AP*TP*TP*GP*TP*GP*GP*CP*C)-3' | dna | 22 | — | — |
| R | 5'-R(*AP*UP*GP*AP*3DRP*GP*GP*CP*CP*AP*CP*AP*AP*UP*AP *AP*CP*UP*AP*UP*AP*GP*GP*CP*AP*UP*A)-3' | rna | 24 | — | — |
Ligands and binding sites
- EFZ · (-)-6-chloro-4-cyclopropylethynyl-4-trifluoromethyl-1, 4-dihydro-2H-3,1-benzoxazin-2-one · ligand · chains A, B
- CA · Calcium ion · metal · 2 copies · chains R
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 888 | 0.85 | 0.87 | 83 | empty |
| 2 | 658 | 0.83 | 0.87 | 75 | empty |
| 3 | 829 | 0.78 | 0.81 | 75 | EFZ |
| 4 | 381 | 0.66 | 0.80 | 33 | empty |
| 5 | 517 | 0.64 | 0.76 | 51 | empty |
Interfaces
6 interfaces between chains.
- A–B · 2651 Ų buried · 24 hydrogen bonds · protein-protein
- D–R · 1034 Ų buried · 99 hydrogen bonds · nucleic-nucleic
- A–D · 997 Ų buried · 11 hydrogen bonds · protein-nucleic
- A–R · 838 Ų buried · 11 hydrogen bonds · protein-nucleic
- B–D · 259 Ų buried · 4 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 4B3O · 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 4B3O · PDBe 4B3O · UniProt P04585
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