Research workbench
HIV-1 reverse transcriptase complex with DNA and inhibitor rmc-233
Analyse HIV-1 reverse transcriptase complex with DNA and inhibitor rmc-233 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7OTK
- Type
- protein + DNA
- Length
- 2,021 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Reverse TRANSCRIPTASE/RIBONUCLEASE H; DNA (5'…
- EC
- 2.7.7.49, 2.7.7.7, 3.1.26.13, 3.1.13.2
- UniProt
- P03366
- Ligands
- 1IA, MG
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 7 distinct chains · 33% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | Reverse TRANSCRIPTASE/RIBONUCLEASE H (EC 2.7.7.49, 2.7.7.7, 3.1.26.13, 3.1.13.2) | protein | 555 | 31% helix, 24% strand | P03366 |
| D | Reverse TRANSCRIPTASE/RIBONUCLEASE H (EC 2.7.7.49, 2.7.7.7, 3.1.26.13, 3.1.13.2) | protein | 411 | 35% helix, 19% strand | P03366 |
| A | Reverse TRANSCRIPTASE/RIBONUCLEASE H (EC 2.7.7.49, 2.7.7.7, 3.1.26.13, 3.1.13.2) | protein | 556 | 32% helix, 24% strand | P03366 |
| B | Reverse TRANSCRIPTASE/RIBONUCLEASE H (EC 2.7.7.49, 2.7.7.7, 3.1.26.13, 3.1.13.2) | protein | 412 | 34% helix, 19% strand | P03366 |
| E | DNA (5'- D(P*GP*GP*TP*CP*GP*GP*CP*GP*CP*CP*CP*GP*AP*AP*CP*AP*GP*GP*GP*AP*CP*TP *G)-3') | dna | 23 | — | — |
| F, P | DNA (5'-D(*CP*AP*GP*TP*CP*CP*CP*TP*GP*TP*TP*CP*GP*GP*(MRG) *CP*GP*CP*CP*(DDG))-3') | dna | 20 | — | — |
| T | DNA (5'- D(P*GP*GP*TP*CP*GP*GP*CP*GP*CP*CP*CP*GP*AP*AP*CP*AP*GP*GP*GP*AP*CP*TP *G)-3') | dna | 24 | — | — |
Ligands and binding sites
- 1IA · (2~{R})-2-[2-(6-aminopurin-9-yl)ethylamino]-3-phosphono-propanoic acid · ligand · chains A, T, P
- MG · Magnesium ion · metal · chains A, P
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 | 914 | 0.87 | 0.89 | 104 | empty |
| 2 | 495 | 0.84 | 0.90 | 55 | empty |
| 3 | 492 | 0.81 | 0.88 | 54 | empty |
| 4 | 389 | 0.81 | 0.90 | 44 | empty |
| 5 | 543 | 0.79 | 0.86 | 53 | empty |
Interfaces
13 interfaces between chains.
- C–D · 2972 Ų buried · 37 hydrogen bonds · protein-protein
- A–B · 2926 Ų buried · 35 hydrogen bonds · protein-protein
- A–T · 1250 Ų buried · 19 hydrogen bonds · protein-nucleic
- C–E · 1172 Ų buried · 16 hydrogen bonds · protein-nucleic
- T–P · 968 Ų buried · 102 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 4 modified (nucleotide modification).
Compared structures
- 7OTK · HIV-1 reverse transcriptase complex with DNA and inhibitor rmc-233 · 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 7OTK · PDBe 7OTK · UniProt P03366
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