Research workbench
HIV-1 wild-type reverse transcriptase-DNA complex with (+)-ftc-tp
Analyse HIV-1 wild-type reverse transcriptase-DNA complex with (+)-ftc-tp in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6UJZ
- Type
- protein + DNA
- Length
- 994 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- P66 reverse TRANSCRIPTASE/RNASEH; P51 reverse TRANSCRIPTASE/RNASEH; Primer DNA; Template…
- EC
- 2.7.7.49, 2.7.7.7, 3.1.26.13
- UniProt
- P04585
- Ligands
- N8G, MG, SO4
- Pockets
- 13 · best druggability 0.85
Structure
x-ray diffraction · 4 distinct chains · 34% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | P66 reverse TRANSCRIPTASE/RNASEH (EC 2.7.7.49, 2.7.7.7, 3.1.26.13) | protein | 553 | 33% helix, 23% strand | P04585 |
| B | P51 reverse TRANSCRIPTASE/RNASEH (EC 2.7.7.49, 2.7.7.7, 3.1.26.13) | protein | 399 | 37% helix, 21% strand | P04585 |
| P | Primer DNA | dna | 18 | — | — |
| T | Template DNA | dna | 24 | — | — |
Ligands and binding sites
- N8G · [[(2~{S},5~{R})-5-(4-azanyl-5-fluoranyl-2-oxidanylidene-pyrimidin-1-yl)-1,3-oxathiolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate · ligand · chains A, P, T
- MG · Magnesium ion · metal · chains A
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 689 | 0.85 | 0.89 | 83 | empty |
| 2 | 421 | 0.82 | 0.91 | 46 | empty |
| 3 | 447 | 0.73 | 0.83 | 47 | empty |
| 4 | 524 | 0.70 | 0.80 | 46 | empty |
| 5 | 531 | 0.70 | 0.80 | 56 | MG, N8G |
Interfaces
6 interfaces between chains.
- A–B · 3020 Ų buried · 34 hydrogen bonds · protein-protein
- A–T · 1342 Ų buried · 11 hydrogen bonds · protein-nucleic
- A–P · 972 Ų buried · 13 hydrogen bonds · protein-nucleic
- P–T · 823 Ų buried · 81 hydrogen bonds · nucleic-nucleic
- B–P · 101 Ų buried · 0 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 6UJZ · HIV-1 wild-type reverse transcriptase-DNA complex with (+)-FTC-TP · 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 6UJZ · PDBe 6UJZ · UniProt P04585
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