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HIV-1 reverse transcriptase in complex with DNA and efda-triphosphate, a translocation-defective rt inhibitor
Analyse HIV-1 reverse transcriptase in complex with DNA and efda-triphosphate, a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5J2M
- Type
- protein + DNA
- Length
- 998 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HIV-1 reverse transcriptase P51 subunit; DNA (5'…
- EC
- 2.7.7.-
- UniProt
- P04585
- Ligands
- 6FN, MG
- Pockets
- 14 · best druggability 0.85
Structure
x-ray diffraction · 4 distinct chains · 35% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | HIV-1 reverse transcriptase P51 subunit (EC 2.7.7.-) | protein | 558 | 32% helix, 24% strand | P04585 |
| B | HIV-1 reverse transcriptase P51 subunit (EC 2.7.7.-) | protein | 398 | 38% helix, 20% strand | P04585 |
| P | DNA (5'- D(*AP*CP*AP*GP*TP*CP*CP*CP*TP*GP*TP*TP*CP*GP*GP*(MRG) P*CP*GP*CP*CP*G)-3') | dna | 18 | — | — |
| T | DNA (27-mer) | dna | 24 | — | — |
Ligands and binding sites
- 6FN · 2'-deoxy-4'-ethynyl-2-fluoroadenosine 5'-(tetrahydrogen triphosphate) · ligand · chains A, P, T
- MG · Magnesium ion · metal · 3 copies · chains A, P
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 702 | 0.85 | 0.89 | 66 | empty |
| 2 | 889 | 0.85 | 0.87 | 80 | empty |
| 3 | 501 | 0.71 | 0.81 | 37 | empty |
| 4 | 366 | 0.71 | 0.83 | 37 | MG, 6FN |
| 5 | 518 | 0.70 | 0.80 | 48 | empty |
Interfaces
6 interfaces between chains.
- A–B · 3028 Ų buried · 31 hydrogen bonds · protein-protein
- A–T · 1385 Ų buried · 15 hydrogen bonds · protein-nucleic
- A–P · 1051 Ų buried · 12 hydrogen bonds · protein-nucleic
- P–T · 851 Ų buried · 80 hydrogen bonds · nucleic-nucleic
- B–P · 118 Ų buried · 0 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 5J2M · HIV-1 reverse transcriptase in complex with DNA and EFdA-triphosphate, a… · 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 5J2M · PDBe 5J2M · UniProt P04585
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