Research workbench
HIV-1 tar loop in complex with TAT:AFF4:P-tefb
Analyse HIV-1 tar loop in complex with TAT:AFF4:P-tefb in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6CYT
- Type
- protein + RNA
- Length
- 670 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cyclin-dependent kinase 9; Cyclin-T1; AF4/FMR2 family member 4; Protein tat; RNA (5'…
- EC
- 2.7.11.22, 2.7.11.23
- UniProt
- P50750, O60563, Q9UHB7, A0A0C5HAL9
- Ligands
- ACE, ZN
- Pockets
- 12 · best druggability 0.75
Structure
x-ray diffraction · 5 distinct chains · 47% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cyclin-dependent kinase 9 (EC 2.7.11.22, 2.7.11.23) | protein | 319 | 37% helix, 15% strand | P50750 |
| B | Cyclin-T1 | protein | 255 | 65% helix, 1% strand | O60563 |
| C | AF4/FMR2 family member 4 | protein | 31 | 29% helix, 6% strand | Q9UHB7 |
| D | Protein tat | protein | 48 | 31% helix, 2% strand | A0A0C5HAL9 |
| N | RNA (5'- R(P*AP*UP*CP*UP*GP*AP*GP*CP*CP*UP*GP*GP*GP*AP*GP*CP*U)-3') | rna | 17 | — | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 100 | 0.75 | 0.95 | 23 | empty |
| 2 | 207 | 0.68 | 0.85 | 23 | empty |
| 3 | 309 | 0.64 | 0.80 | 34 | empty |
| 4 | 548 | 0.60 | 0.74 | 44 | empty |
| 5 | 250 | 0.58 | 0.78 | 30 | empty |
Interfaces
7 interfaces between chains.
- B–D · 1715 Ų buried · 11 hydrogen bonds · protein-protein
- B–C · 1350 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 1030 Ų buried · 10 hydrogen bonds · protein-protein
- A–D · 269 Ų buried · 4 hydrogen bonds · protein-protein
- B–N · 240 Ų buried · 4 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 1 covalent, 1 modified (covalent ligand, phosphorylation).
Compared structures
- 6CYT · HIV-1 TAR loop in complex with Tat:AFF4:P-TEFb · the same entry in another collection · chain N against N, TM-score 1.00
- P50750 · AlphaFold monomer V2.0 prediction for cyclin-dependent kinase 9 (P50750) · a predicted model of the same protein · chain A against A, TM-score 0.99
- O60563 · AlphaFold monomer V2.0 prediction for cyclin-T1 (O60563) · a predicted model of the same protein · chain B against A, TM-score 0.95
- Q9UHB7 · AlphaFold monomer V2.0 prediction for AF4/FMR2 family member 4 (Q9UHB7) · a predicted model of the same protein · chain C against A, TM-score 0.54
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 P50750
- Every structure of UniProt O60563
- Every structure of UniProt Q9UHB7
- Every structure of UniProt A0A0C5HAL9
- Elsewhere: RCSB PDB 6CYT · PDBe 6CYT · UniProt P50750 · UniProt O60563 · UniProt Q9UHB7 · UniProt A0A0C5HAL9
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