MolNFT v1 · #69272 · protein + DNA
Crystal structure of azt-resistant HIV-1 reverse transcriptase crosslinked to post-translocation aztmp-terminated DNA (complex P)
3KLH · Reverse TRANSCRIPTASE/RIBONUCLEASE H: “Crystal structure of azt-resistant HIV-1 reverse transcriptase crosslinked to post-translocation…”. X-ray diffraction, 1 ligand (MG), 20 pockets (best druggability 0.86). MolNFT v1 #69272 on…
- PDB
- 3KLH
- Type
- protein + DNA
- Length
- 1,467 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Reverse TRANSCRIPTASE/RIBONUCLEASE H; P51 rt; Monoclonal antibody, heavy chain…
- EC
- 2.7.7.49, 2.7.7.7, 3.1.26.4
- UniProt
- P03366
- Ligands
- MG
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 6 distinct chains · 23% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Reverse TRANSCRIPTASE/RIBONUCLEASE H (EC 2.7.7.49, 2.7.7.7, 3.1.26.4) | protein | 558 | 30% helix, 22% strand | P03366 |
| B | P51 rt | protein | 428 | 30% helix, 17% strand | P03366 |
| C | Monoclonal antibody, heavy chain | protein | 211 | 5% helix, 49% strand | — |
| D | Monoclonal antibody, light chain | protein | 225 | 4% helix, 52% strand | — |
| E | DNA (5'- D(*AP*T*GP*CP*TP*AP*GP*GP*CP*GP*CP*CP*CP*GP*AP*AP*CP*AP*GP*GP*GP*AP*C P*TP*GP*TP*G)-3') | dna | 24 | — | — |
| F | DNA (5'- D(*AP*CP*AP*GP*TP*CP*CP*CP*TP*GP*TP*TP*CP*GP*GP*(MRG) P*CP*GP*CP*CP*(ATM))-3') | dna | 21 | — | — |
Ligands and binding sites
- MG · Magnesium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1028 | 0.86 | 0.88 | 102 | empty |
| 2 | 1069 | 0.84 | 0.85 | 86 | empty |
| 3 | 747 | 0.77 | 0.81 | 56 | empty |
| 4 | 300 | 0.72 | 0.85 | 38 | empty |
| 5 | 415 | 0.64 | 0.78 | 40 | empty |
Interfaces
9 interfaces between chains.
- A–B · 3001 Ų buried · 40 hydrogen bonds · protein-protein
- C–D · 1887 Ų buried · 13 hydrogen bonds · protein-protein
- A–E · 1340 Ų buried · 10 hydrogen bonds · protein-nucleic
- A–F · 1001 Ų buried · 18 hydrogen bonds · protein-nucleic
- E–F · 961 Ų buried · 73 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 4 disulfide, 2 modified (disulfide, nucleotide modification).
Compared structures
- 3KLH · Crystal structure of AZT-Resistant HIV-1 Reverse Transcriptase crosslinked to… · 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 3KLH · PDBe 3KLH · UniProt P03366
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