MolNFT v1 · #181331 · protein + DNA
Structure of HIV-1 reverse transcriptase in complex with DNA, dctp, and CA(2+) ion
7LRM · Reverse transcriptase P66: “Structure of HIV-1 reverse transcriptase in complex with DNA, dctp, and CA(2+) ion”. X-ray diffraction, 5 ligands (DCP, GLC, FRU), 20 pockets (best druggability 0.86). MolNFT v1 #181331 on GenesisL1: 3D…
- PDB
- 7LRM
- Type
- protein + DNA
- Length
- 2,001 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
- DCP, GLC, FRU, CA, SO4
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 4 distinct chains · 34% helix, 22% 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 | 553 | 32% helix, 24% strand | P03366 |
| B | Reverse transcriptase P51 (EC 2.7.7.49) | protein | 415 | 36% helix, 20% strand | P03366 |
| D | Reverse transcriptase P51 (EC 2.7.7.49) | protein | 410 | 35% helix, 20% strand | P03366 |
| F, E | DNA/RNA (38-mer) | dna | 35 | — | — |
Ligands and binding sites
- DCP · 2'-deoxycytidine-5'-triphosphate · ligand · 2 copies · chains A, E, C, F
- GLC · alpha-D-glucopyranose · sugar · 2 copies · chains B, D
- FRU · beta-D-fructofuranose · sugar · 2 copies · chains B, D, F
- CA · Calcium ion · metal · 2 copies · chains A, C
- SO4 · Sulfate ion · ion · 2 copies · chains A, C
- GOL · Glycerol · additive · 12 copies · chains A, B, C, D, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1020 | 0.86 | 0.87 | 84 | GOL |
| 2 | 1160 | 0.85 | 0.86 | 90 | GOL |
| 3 | 988 | 0.84 | 0.85 | 94 | GLC, FRU, GOL |
| 4 | 1084 | 0.83 | 0.84 | 93 | GOL |
| 5 | 1084 | 0.79 | 0.81 | 93 | empty |
Interfaces
8 interfaces between chains.
- A–B · 3023 Ų buried · 36 hydrogen bonds · protein-protein
- C–D · 2992 Ų buried · 35 hydrogen bonds · protein-protein
- A–E · 2082 Ų buried · 24 hydrogen bonds · protein-nucleic
- C–F · 1959 Ų buried · 25 hydrogen bonds · protein-nucleic
- B–C · 429 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (nucleotide modification).
Compared structures
- 7LRM · Structure of HIV-1 Reverse Transcriptase in complex with DNA, dCTP, 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 7LRM · PDBe 7LRM · UniProt P03366
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