MolNFT v1 · #181276 · protein
Crystal structure of HIV-1 rt in complex with nbd-14189
7LPW · Reverse transcriptase P66: “Crystal structure of HIV-1 rt in complex with nbd-14189”. X-ray diffraction, 2 ligands (YBA, SO4), 17 pockets (best druggability 0.77). MolNFT v1 #181276 on GenesisL1: 3D structure, binding sites and…
- PDB
- 7LPW
- Type
- protein
- Length
- 968 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Reverse transcriptase P66; Reverse transcriptase P51
- EC
- 2.7.7.49
- UniProt
- P03366
- Ligands
- YBA, SO4
- Pockets
- 17 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 33% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Reverse transcriptase P66 (EC 2.7.7.49) | protein | 556 | 32% helix, 24% strand | P03366 |
| B | Reverse transcriptase P51 | protein | 412 | 35% helix, 20% strand | P03366 |
Ligands and binding sites
- YBA · ~{N}-[(1~{S})-2-azanyl-1-[4-(hydroxymethyl)-1,3-thiazol-2-yl]ethyl]-5-[3-fluoranyl-4-(trifluoromethyl)phenyl]-1~{H}-pyrrole-2-carboxamide · ligand · chains A
- SO4 · Sulfate ion · ion · 4 copies · chains A, B
- DMS · Dimethyl sulfoxide · additive · 3 copies · chains A, B
- EDO · 1,2-ethanediol · additive · chains 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, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 722 | 0.77 | 0.82 | 72 | empty |
| 2 | 605 | 0.75 | 0.82 | 61 | empty |
| 3 | 480 | 0.68 | 0.79 | 39 | empty |
| 4 | 141 | 0.66 | 0.87 | 20 | YBA |
| 5 | 491 | 0.65 | 0.77 | 47 | empty |
Interfaces
1 interface between chains.
- A–B · 2918 Ų buried · 30 hydrogen bonds · protein-protein
Compared structures
- 7LPW · Crystal Structure of HIV-1 RT in Complex with NBD-14189 · 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 7LPW · PDBe 7LPW · UniProt P03366
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