MolNFT v1 · #69269 · protein + DNA
Crystal structure of azt-resistant HIV-1 reverse transcriptase crosslinked to a dsdna with a bound excision product, aztppppa
3KLE · Reverse TRANSCRIPTASE/RIBONUCLEASE H: “Crystal structure of azt-resistant HIV-1 reverse transcriptase crosslinked to a dsdna with a bound excision…”. X-ray diffraction, 4 ligands (ZP4, GLC, Z9N), 20 pockets (best druggability 0.88).…
- PDB
- 3KLE
- Type
- protein + DNA
- Length
- 4,106 residues
- Chains
- 16
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Reverse TRANSCRIPTASE/RIBONUCLEASE H; P51 rt; DNA (25-mer); DNA (5'…
- EC
- 2.7.7.49, 2.7.7.7, 3.1.26.4
- UniProt
- P03366
- Ligands
- ZP4, GLC, Z9N, MG
- Pockets
- 20 · best druggability 0.88
Structure
x-ray diffraction · 5 distinct chains · 33% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E, I, M | Reverse TRANSCRIPTASE/RIBONUCLEASE H (EC 2.7.7.49, 2.7.7.7, 3.1.26.4) | protein | 560 | 31% helix, 20% strand | P03366 |
| B | P51 rt | protein | 425 | 35% helix, 19% strand | P03366 |
| F, J, N | P51 rt | protein | 419 | 36% helix, 19% strand | P03366 |
| C, G, K, O | DNA (25-mer) | dna | 25 | — | — |
| D, H, L, P | DNA (5'- D(*AP*CP*AP*GP*TP*CP*CP*CP*TP*GP*TP*TP*CP*GP*GP*(MRG) P*CP*GP*CP*CP*(2DA))-3') | dna | 21 | — | — |
Ligands and binding sites
- ZP4 · [[[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-dihydroxy-oxolan-2-yl]methoxy-hydroxy-phosphoryl]oxy-hydroxy-phosphoryl]oxy-hydroxy-phosphoryl] [(2S,3S,5R)-3-azido-5-(5-methyl-2,4-dioxo-pyrimidin-1-yl)oxolan-2-yl]methyl hydrogen phosphate · ligand · 4 copies · chains A, C, D, E, G, H, I, K, L, M, O, P
- GLC · alpha-D-glucopyranose · sugar · chains E, J
- Z9N · alpha-D-fructofuranose · sugar · chains E, J
- MG · Magnesium ion · metal · 8 copies · chains A, C, E, G, I, K, M, O
- GOL · Glycerol · additive · 2 copies · chains B, 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 | 1083 | 0.88 | 0.90 | 118 | empty |
| 2 | 822 | 0.86 | 0.89 | 79 | empty |
| 3 | 577 | 0.83 | 0.89 | 60 | empty |
| 4 | 534 | 0.82 | 0.89 | 50 | empty |
| 5 | 359 | 0.82 | 0.91 | 40 | empty |
Interfaces
30 interfaces between chains.
- E–F · 2940 Ų buried · 37 hydrogen bonds · protein-protein
- A–B · 2933 Ų buried · 38 hydrogen bonds · protein-protein
- I–J · 2932 Ų buried · 39 hydrogen bonds · protein-protein
- M–N · 2893 Ų buried · 35 hydrogen bonds · protein-protein
- A–C · 1351 Ų buried · 11 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 8 modified (nucleotide modification).
Compared structures
- 3KLE · Crystal structure of AZT-resistant HIV-1 Reverse Transcriptase crosslinked to a DSDNA… · 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 3KLE · PDBe 3KLE · UniProt P03366
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