Research workbench
Crystal structure of HIV-1 reverse transcriptase with a double stranded DNA in complex with fragment 048 at the transient P-pocket.
Analyse Crystal structure of HIV-1 reverse transcriptase with a double stranded DNA in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7OXQ
- Type
- protein + DNA
- Length
- 2,016 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Reverse TRANSCRIPTASE/RIBONUCLEASE H; Gag-pol polyprotein; DNA (28-mer); DNA (5'…
- EC
- 2.7.7.49, 2.7.7.7, 3.1.26.13, 3.1.13.2, 3.4.23.16, 2.7.7.-, 3.1.-.-
- UniProt
- P03366
- Ligands
- 2NU, CD
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 8 distinct chains · 34% helix, 22% 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, 3.1.13.2) | protein | 555 | 33% helix, 23% strand | P03366 |
| B | Gag-pol polyprotein (EC 3.4.23.16, 2.7.7.49, 2.7.7.7, 3.1.26.13, 3.1.13.2, 2.7.7.-, 3.1.-.-) | protein | 418 | 34% helix, 20% strand | P03366 |
| T | DNA (28-mer) | dna | 23 | — | — |
| P | DNA (5'- D(*AP*CP*AP*GP*TP*CP*CP*CP*TP*GP*TP*TP*CP*GP*GP*GP*CP*GP*CP*CP*G)- 3') | dna | 21 | — | — |
| C | Reverse TRANSCRIPTASE/RIBONUCLEASE H (EC 2.7.7.49, 2.7.7.7, 3.1.26.13, 3.1.13.2) | protein | 551 | 32% helix, 23% strand | P03366 |
| D | Gag-pol polyprotein (EC 3.4.23.16, 2.7.7.49, 2.7.7.7, 3.1.26.13, 3.1.13.2, 2.7.7.-, 3.1.-.-) | protein | 406 | 37% helix, 21% strand | P03366 |
| E | DNA (28-mer) | dna | 22 | — | — |
| F | DNA (5'- D(*AP*CP*AP*GP*TP*CP*CP*CP*TP*GP*TP*TP*CP*GP*GP*GP*CP*GP*CP*CP*G)- 3') | dna | 20 | — | — |
Ligands and binding sites
- 2NU · 2-(4-bromanylpyrazol-1-yl)-~{N}-cyclopropyl-~{N}-methyl-ethanamide · ligand · chains C, E, F
- CD · Cadmium ion · metal · 21 copies · chains A, B, T, P, C, E, 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, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1062 | 0.87 | 0.88 | 126 | empty |
| 2 | 659 | 0.84 | 0.88 | 65 | empty |
| 3 | 370 | 0.84 | 0.93 | 41 | empty |
| 4 | 382 | 0.83 | 0.92 | 51 | empty |
| 5 | 310 | 0.74 | 0.86 | 41 | empty |
Interfaces
13 interfaces between chains.
- A–B · 2929 Ų buried · 37 hydrogen bonds · protein-protein
- C–D · 2922 Ų buried · 34 hydrogen bonds · protein-protein
- A–T · 1306 Ų buried · 16 hydrogen bonds · protein-nucleic
- A–P · 1197 Ų buried · 20 hydrogen bonds · protein-nucleic
- C–E · 1135 Ų buried · 12 hydrogen bonds · protein-nucleic
Compared structures
- 7OXQ · Crystal structure of HIV-1 reverse transcriptase with a double stranded DNA in complex… · 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 7OXQ · PDBe 7OXQ · UniProt P03366
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