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Crystal structure of HIV-1 reverse transcriptase with a double stranded DNA showing a transient P-pocket
Analyse Crystal structure of HIV-1 reverse transcriptase with a double stranded DNA… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7OZ2
- Type
- protein + DNA
- Length
- 2,020 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
- CD, MG, SO4
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 7 distinct chains · 33% 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 | 417 | 35% helix, 19% strand | P03366 |
| T | DNA (28-mer) | dna | 25 | — | — |
| P, 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 | 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 | 31% helix, 24% 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 | 36% helix, 20% strand | P03366 |
| E | DNA (28-mer) | dna | 24 | — | — |
Ligands and binding sites
- CD · Cadmium ion · metal · 27 copies · chains A, P, B, T, C, E, D, F
- MG · Magnesium ion · metal · chains C, F
- SO4 · Sulfate ion · ion · 2 copies · chains A, P, B
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 | 966 | 0.86 | 0.88 | 110 | empty |
| 2 | 779 | 0.84 | 0.88 | 67 | empty |
| 3 | 809 | 0.84 | 0.87 | 83 | empty |
| 4 | 470 | 0.83 | 0.90 | 46 | empty |
| 5 | 336 | 0.74 | 0.85 | 43 | empty |
Interfaces
13 interfaces between chains.
- A–B · 2994 Ų buried · 35 hydrogen bonds · protein-protein
- C–D · 2774 Ų buried · 33 hydrogen bonds · protein-protein
- A–T · 1291 Ų buried · 12 hydrogen bonds · protein-nucleic
- A–P · 1174 Ų buried · 17 hydrogen bonds · protein-nucleic
- C–E · 1148 Ų buried · 12 hydrogen bonds · protein-nucleic
Compared structures
- 7OZ2 · Crystal structure of HIV-1 reverse transcriptase with a double stranded DNA showing a… · 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 7OZ2 · PDBe 7OZ2 · UniProt P03366
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