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HIV-1 reverse transcriptase with bound fragment at the 428 site
Analyse HIV-1 reverse transcriptase with bound fragment at the 428 site in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4IDK
- Type
- protein
- Length
- 968 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, 3.1.26.13
- UniProt
- P03366
- Ligands
- T27, 1FE, MG
- Pockets
- 13 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 33% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Reverse TRANSCRIPTASE/RIBONUCLEASE H (EC 2.7.7.49, 2.7.7.7, 3.1.26.13) | protein | 556 | 32% helix, 24% strand | P03366 |
| B | P51 rt (EC 2.7.7.49, 2.7.7.7, 3.1.26.13) | protein | 412 | 35% helix, 20% strand | P03366 |
Ligands and binding sites
- T27 · 4-{[4-({4-[(E)-2-cyanoethenyl]-2,6-dimethylphenyl}amino)pyrimidin-2-yl]amino}benzonitrile · ligand · chains A, B
- 1FE · N-(2-oxo-2,3-dihydro-1H-benzimidazol-5-yl)glycinamide · ligand · chains A
- MG · Magnesium ion · metal · chains A
- DMS · Dimethyl sulfoxide · additive · 16 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1043 | 0.81 | 0.82 | 114 | T27, DMS |
| 2 | 494 | 0.72 | 0.81 | 40 | empty |
| 3 | 661 | 0.71 | 0.78 | 50 | empty |
| 4 | 289 | 0.70 | 0.84 | 34 | DMS |
| 5 | 297 | 0.59 | 0.78 | 42 | DMS |
Interfaces
1 interface between chains.
- A–B · 2727 Ų buried · 33 hydrogen bonds · protein-protein
Compared structures
- 4IDK · HIV-1 reverse transcriptase with bound fragment at the 428 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 4IDK · PDBe 4IDK · UniProt P03366
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