MolNFT v1 · #89125 · protein
Crystal structure of HIV-1 reverse transcriptase (rt) with polymorphism mutation K172A and K173A
4DG1 · Reverse transcriptase P66 subunit: “Crystal structure of HIV-1 reverse transcriptase (rt) with polymorphism mutation K172A and K173A”. X-ray diffraction, 1 ligand (MG), 16 pockets (best druggability 0.76). MolNFT v1 #89125 on…
- PDB
- 4DG1
- Type
- protein
- Length
- 967 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Reverse transcriptase P66 subunit; Reverse transcriptase P51 subunit
- EC
- 2.7.7.49, 2.7.7.7
- UniProt
- P03366
- Ligands
- MG
- Pockets
- 16 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 32% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Reverse transcriptase P66 subunit (EC 2.7.7.49, 2.7.7.7) | protein | 549 | 31% helix, 24% strand | P03366 |
| B | Reverse transcriptase P51 subunit (EC 2.7.7.49, 2.7.7.7) | protein | 418 | 34% helix, 19% strand | P03366 |
Ligands and binding sites
- MG · Magnesium ion · metal · 4 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 14 copies · chains A, B
- GOL · Glycerol · additive · 6 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 770 | 0.76 | 0.80 | 61 | GOL, EDO |
| 2 | 519 | 0.74 | 0.82 | 57 | empty |
| 3 | 188 | 0.69 | 0.87 | 26 | empty |
| 4 | 403 | 0.66 | 0.79 | 41 | EDO |
| 5 | 299 | 0.61 | 0.79 | 59 | MG, EDO |
Interfaces
1 interface between chains.
- A–B · 2759 Ų buried · 27 hydrogen bonds · protein-protein
Compared structures
- 4DG1 · Crystal structure of HIV-1 reverse transcriptase (RT) with polymorphism mutation K172A… · 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 4DG1 · PDBe 4DG1 · UniProt P03366
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