Research workbench
Crystal structure of HIV-1 tat complexed with ATP-bound human P-tefb
Analyse Crystal structure of HIV-1 tat complexed with ATP-bound human P-tefb in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3MIA
- Type
- protein
- Length
- 620 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cell division protein kinase 9; Cyclin-T1; Protein tat
- EC
- 2.7.11.22, 2.7.11.23
- UniProt
- P50750, O60563, P04608
- Ligands
- ANP, ZN, MG
- Pockets
- 9 · best druggability 0.68
Structure
x-ray diffraction · 3 distinct chains · 48% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cell division protein kinase 9 (EC 2.7.11.22, 2.7.11.23) | protein | 325 | 38% helix, 14% strand | P50750 |
| B | Cyclin-T1 | protein | 247 | 64% helix, 0% strand | O60563 |
| C | Protein tat | protein | 48 | 23% helix, 2% strand | P04608 |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · chains A
- ZN · Zinc ion · metal · 2 copies · chains C, B
- MG · Magnesium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 484 | 0.68 | 0.79 | 64 | empty |
| 2 | 324 | 0.63 | 0.79 | 36 | ANP |
| 3 | 197 | 0.54 | 0.79 | 25 | empty |
| 4 | 131 | 0.47 | 0.78 | 15 | empty |
| 5 | 71 | 0.46 | 0.82 | 20 | empty |
Interfaces
3 interfaces between chains.
- B–C · 1448 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 1022 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 227 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (phosphorylation).
Compared structures
- 3MIA · Crystal structure of HIV-1 Tat complexed with ATP-bound human P-TEFb · the same entry in another collection · chain A against A, TM-score 1.00
- O60563 · AlphaFold monomer V2.0 prediction for cyclin-T1 (O60563) · a predicted model of the same protein · chain B against A, TM-score 0.97
- 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 0.96
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 P04608
- Elsewhere: RCSB PDB 3MIA · PDBe 3MIA · UniProt P50750 · UniProt O60563 · UniProt P04608
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