Research workbench
Structure of HIV-1 reverse transcriptase in complex with DNA, L-dttp, and CA(2+) ion
Analyse Structure of HIV-1 reverse transcriptase in complex with DNA, L-dttp, and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7LSK
- Type
- protein + DNA
- Length
- 2,002 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Reverse transcriptase P66; Reverse transcriptase P51; DNA/RNA (38-mer)
- EC
- 2.7.7.49, 2.7.7.7, 3.1.26.13
- UniProt
- P03366
- Ligands
- XRF, GLC, FRU, CA, SO4, NH4
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 3 distinct chains · 33% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Reverse transcriptase P66 (EC 2.7.7.49, 2.7.7.7, 3.1.26.13) | protein | 554 | 31% helix, 23% strand | P03366 |
| B, D | Reverse transcriptase P51 | protein | 412 | 35% helix, 19% strand | P03366 |
| F, E | DNA/RNA (38-mer) | dna | 35 | — | — |
Ligands and binding sites
- XRF · 1-{2-deoxy-5-O-[(S)-hydroxy{[(s)-hydroxy(phosphonooxy) phosphoryl]oxy}phosphoryl]-beta-L-erythro-pentofuranosyl}-5-methylpyrimidine-2,4(1H,3H)-dione · ligand · 2 copies · chains A, E, C, F
- GLC · alpha-D-glucopyranose · sugar · 2 copies · chains D, B
- FRU · beta-D-fructofuranose · sugar · 2 copies · chains D, B
- CA · Calcium ion · metal · 2 copies · chains A, C
- SO4 · Sulfate ion · ion · 2 copies · chains A, C
- NH4 · Ammonium ion · ion · 2 copies · chains A, C
- GOL · Glycerol · additive · 3 copies · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
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 | 1153 | 0.85 | 0.86 | 97 | empty |
| 2 | 1066 | 0.83 | 0.84 | 97 | GLC, FRU |
| 3 | 1106 | 0.82 | 0.84 | 98 | GLC, FRU |
| 4 | 709 | 0.82 | 0.86 | 60 | GOL |
| 5 | 490 | 0.80 | 0.88 | 48 | empty |
Interfaces
7 interfaces between chains.
- A–B · 3032 Ų buried · 36 hydrogen bonds · protein-protein
- C–D · 2996 Ų buried · 37 hydrogen bonds · protein-protein
- C–F · 2007 Ų buried · 26 hydrogen bonds · protein-nucleic
- A–E · 1996 Ų buried · 29 hydrogen bonds · protein-nucleic
- B–C · 293 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (nucleotide modification).
Compared structures
- 7LSK · Structure of HIV-1 Reverse Transcriptase in complex with DNA, L-dTTP, and CA(2+) ion · 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 P03366
- Elsewhere: RCSB PDB 7LSK · PDBe 7LSK · UniProt P03366
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