Research workbench
Crystal structure of HIV-1 K103N mutant reverse transcriptase in complex with GW564511.
Analyse Crystal structure of HIV-1 K103N mutant reverse transcriptase in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3DM2
- Type
- protein
- Length
- 932 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Reverse TRANSCRIPTASE/RIBONUCLEASE H; P51 rt
- EC
- 2.7.7.49, 2.7.7.7, 3.1.26.4
- UniProt
- P04585
- Ligands
- GWE, PO4
- Pockets
- 17 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 34% helix, 24% 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 | 532 | 32% helix, 25% strand | P04585 |
| B | P51 rt | protein | 400 | 36% helix, 21% strand | P04585 |
Ligands and binding sites
- GWE · N-{4-[amino(dihydroxy)-lambda~4~-sulfanyl]-2-methylphenyl}-2-(4-chloro-2-{[3-fluoro-5-(trifluoromethyl)phenyl]carbonyl}phenoxy)acetamide · ligand · chains A
- PO4 · Phosphate ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1102 | 0.78 | 0.80 | 96 | empty |
| 2 | 202 | 0.74 | 0.89 | 28 | GWE |
| 3 | 536 | 0.74 | 0.82 | 49 | empty |
| 4 | 173 | 0.61 | 0.83 | 29 | empty |
| 5 | 341 | 0.57 | 0.76 | 40 | empty |
Interfaces
1 interface between chains.
- A–B · 2664 Ų buried · 34 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (oxidation).
Compared structures
- 3DM2 · Crystal structure of HIV-1 K103N mutant reverse transcriptase in complex with GW564511. · 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 P04585
- Elsewhere: RCSB PDB 3DM2 · PDBe 3DM2 · UniProt P04585
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