MolNFT v1 · #97483 · protein
HIV-1 reverse transcriptase with bound fragment at nnrti adjacent site
4KFB · Reverse TRANSCRIPTASE/RIBONUCLEASE H, exoribonuclea P66 rt: “HIV-1 reverse transcriptase with bound fragment at nnrti adjacent site”. X-ray diffraction, 2 ligands (1QP, T27), 15 pockets (best druggability 0.80). MolNFT v1 #97483 on…
- PDB
- 4KFB
- Type
- protein
- Length
- 968 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Reverse TRANSCRIPTASE/RIBONUCLEASE H, exoribonuclea P66 rt; P51 rt
- EC
- 2.7.7.49, 2.7.7.7, 3.1.26.13, 3.1.13.2
- UniProt
- P03366
- Ligands
- 1QP, T27
- Pockets
- 15 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 33% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Reverse TRANSCRIPTASE/RIBONUCLEASE H, exoribonuclea P66 rt (EC 2.7.7.49, 2.7.7.7, 3.1.26.13, 3.1.13.2) | protein | 556 | 32% helix, 23% strand | P03366 |
| B | P51 rt | protein | 412 | 35% helix, 20% strand | P03366 |
Ligands and binding sites
- 1QP · ethyl pyrazolo[1,5-a]pyridine-3-carboxylate · ligand · chains A, B
- T27 · 4-{[4-({4-[(E)-2-cyanoethenyl]-2,6-dimethylphenyl}amino)pyrimidin-2-yl]amino}benzonitrile · ligand · chains A, B
- DMS · Dimethyl sulfoxide · additive · 10 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 906 | 0.80 | 0.82 | 84 | 1QP, DMS, T27 |
| 2 | 552 | 0.74 | 0.82 | 42 | empty |
| 3 | 738 | 0.70 | 0.77 | 56 | empty |
| 4 | 196 | 0.65 | 0.84 | 26 | empty |
| 5 | 278 | 0.57 | 0.77 | 38 | DMS |
Interfaces
1 interface between chains.
- A–B · 2673 Ų buried · 29 hydrogen bonds · protein-protein
Compared structures
- 4KFB · HIV-1 reverse transcriptase with bound fragment at NNRTI adjacent site · 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 4KFB · PDBe 4KFB · UniProt P03366
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