MolNFT v1 · #102618 · protein
Crystal structure of HIV-1 tat complexed with human P-tefb and AFF4
4OR5 · Cyclin-dependent kinase 9: “Crystal structure of HIV-1 tat complexed with human P-tefb and AFF4”. X-ray diffraction, 3 ligands (YT3, ZN, SO4), 20 pockets (best druggability 0.80). MolNFT v1 #102618 on GenesisL1: 3D structure…
- PDB
- 4OR5
- Type
- protein
- Length
- 1,328 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cyclin-dependent kinase 9; Cyclin-T1; Protein tat; AF4/FMR2 family member 4
- EC
- 2.7.11.22, 2.7.11.23
- UniProt
- P50750, O60563, P04608, Q9UHB7
- Ligands
- YT3, ZN, SO4
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · 6 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 | 320 | 34% helix, 14% strand | P50750 |
| B | Cyclin-T1 | protein | 256 | 64% helix, 1% strand | O60563 |
| C, H | Protein tat | protein | 48 | 33% helix, 2% strand | P04608 |
| E, J | AF4/FMR2 family member 4 | protein | 38 | 37% helix, 5% strand | Q9UHB7 |
| F | Cyclin-dependent kinase 9 (EC 2.7.11.22, 2.7.11.23) | protein | 325 | 36% helix, 14% strand | P50750 |
| G | Cyclin-T1 | protein | 255 | 62% helix, 1% strand | O60563 |
Ligands and binding sites
- YT3 · Yttrium (III) ion · metal · 16 copies · chains A, B, E, F, G, J
- ZN · Zinc ion · metal · 4 copies · chains C, B, H, G
- SO4 · Sulfate ion · ion · 4 copies · chains A, B, E, F, G, J
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1076 | 0.80 | 0.81 | 97 | empty |
| 2 | 461 | 0.74 | 0.83 | 57 | empty |
| 3 | 449 | 0.72 | 0.82 | 57 | empty |
| 4 | 337 | 0.62 | 0.78 | 36 | SO4 |
| 5 | 306 | 0.61 | 0.79 | 33 | SO4 |
Interfaces
16 interfaces between chains.
- G–H · 1828 Ų buried · 20 hydrogen bonds · protein-protein
- B–C · 1805 Ų buried · 17 hydrogen bonds · protein-protein
- G–J · 1727 Ų buried · 21 hydrogen bonds · protein-protein
- B–E · 1719 Ų buried · 19 hydrogen bonds · protein-protein
- F–G · 1227 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (phosphorylation).
Compared structures
- 4OR5 · Crystal structure of HIV-1 Tat complexed with human P-TEFb and AFF4 · the same entry in another collection · chain J against J, 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 0.98
- O60563 · AlphaFold monomer V2.0 prediction for cyclin-T1 (O60563) · a predicted model of the same protein · chain G 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
- Every structure of UniProt Q9UHB7
- Elsewhere: RCSB PDB 4OR5 · PDBe 4OR5 · UniProt P50750 · UniProt O60563 · UniProt P04608 · UniProt Q9UHB7
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