MolNFT v1 · #71439 · protein
HIV-1 reverse transcriptase in complex with TMC125
3MEC · P66 reverse transcriptase: “HIV-1 reverse transcriptase in complex with TMC125”. X-ray diffraction, 2 ligands (65B, SO4), 16 pockets (best druggability 0.80). MolNFT v1 #71439 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 3MEC
- Type
- protein
- Length
- 951 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- P66 reverse transcriptase; P51 reverse transcriptase
- EC
- 2.7.7.49
- UniProt
- P04585
- Ligands
- 65B, SO4
- Pockets
- 16 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 34% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | P66 reverse transcriptase (EC 2.7.7.49) | protein | 550 | 32% helix, 23% strand | P04585 |
| B | P51 reverse transcriptase (EC 2.7.7.49) | protein | 401 | 38% helix, 19% strand | P04585 |
Ligands and binding sites
- 65B · 4-({6-amino-5-bromo-2-[(4-cyanophenyl)amino]pyrimidin-4-yl}oxy)-3,5-dimethylbenzonitrile · ligand · chains A, B
- SO4 · Sulfate ion · ion · 5 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, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 987 | 0.80 | 0.81 | 99 | 65B |
| 2 | 282 | 0.69 | 0.83 | 36 | empty |
| 3 | 405 | 0.67 | 0.80 | 36 | empty |
| 4 | 187 | 0.59 | 0.81 | 32 | empty |
| 5 | 143 | 0.53 | 0.81 | 27 | empty |
Interfaces
1 interface between chains.
- A–B · 2856 Ų buried · 32 hydrogen bonds · protein-protein
Compared structures
- 3MEC · HIV-1 Reverse Transcriptase in Complex with TMC125 · 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 3MEC · PDBe 3MEC · UniProt P04585
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