Research workbench
Structure of HIV-1 reverse transcriptase initiation complex core with efavirenz
Analyse Structure of HIV-1 reverse transcriptase initiation complex core with efavirenz in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7KJW
- Type
- protein + RNA
- Length
- 993 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Reverse TRANSCRIPTASE/RIBONUCLEASE H; Reverse transcriptase P51 subunit; HIV-1 viral RNA…
- EC
- 2.7.7.49, 2.7.7.7, 3.1.26.13
- UniProt
- P03366
- Ligands
- EFZ, MG
- Pockets
- 13 · best druggability 0.85
Structure
electron microscopy · 4 distinct chains · 33% helix, 20% 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) | protein | 543 | 31% helix, 22% strand | P03366 |
| B | Reverse transcriptase P51 subunit | protein | 406 | 36% helix, 17% strand | P03366 |
| C | HIV-1 viral RNA fragment | rna | 22 | — | — |
| D | TRNA lysine 3 fragment with gnra tetraloop | rna | 22 | — | — |
Ligands and binding sites
- EFZ · (-)-6-chloro-4-cyclopropylethynyl-4-trifluoromethyl-1, 4-dihydro-2H-3,1-benzoxazin-2-one · ligand · chains A, B
- MG · Magnesium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1168 | 0.85 | 0.86 | 109 | MG |
| 2 | 1104 | 0.81 | 0.82 | 108 | empty |
| 3 | 560 | 0.74 | 0.81 | 57 | EFZ |
| 4 | 225 | 0.60 | 0.81 | 32 | empty |
| 5 | 234 | 0.54 | 0.77 | 40 | empty |
Interfaces
6 interfaces between chains.
- A–B · 2802 Ų buried · 25 hydrogen bonds · protein-protein
- C–D · 1096 Ų buried · 117 hydrogen bonds · nucleic-nucleic
- A–D · 640 Ų buried · 5 hydrogen bonds · protein-nucleic
- A–C · 556 Ų buried · 5 hydrogen bonds · protein-nucleic
- B–C · 90 Ų buried · 1 hydrogen bond · protein-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 7KJW · Structure of HIV-1 reverse transcriptase initiation complex core with efavirenz · 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 7KJW · PDBe 7KJW · UniProt P03366
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