MolNFT v1 · #52494 · protein + RNA
Structural basis of transcription activation by the cyclin T1-tat-tar RNA complex from eiav
2W2H · Cyclin-T1: “Structural basis of transcription activation by the cyclin T1-tat-tar RNA complex from eiav”. X-ray diffraction, 1 ligand (MN), 15 pockets (best druggability 0.73). MolNFT v1 #52494 on GenesisL1: 3D structure, binding…
- PDB
- 2W2H
- Type
- protein + RNA
- Length
- 625 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cyclin-T1; Protein tat; 5'-R(*GP*CP*UP*CP*AP*GP*AP*UP*CP*UP…
- UniProt
- Q9XT26, P20920
- Ligands
- MN
- Pockets
- 15 · best druggability 0.73
Structure
x-ray diffraction · 4 distinct chains · 47% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cyclin-T1 | protein | 263 | 49% helix, 0% strand | Q9XT26 |
| B | Cyclin-T1 | protein | 260 | 48% helix, 0% strand | Q9XT26 |
| C, D | Protein tat | protein | 29 | 17% helix, 0% strand | P20920 |
| R, S | 5'-R(*GP*CP*UP*CP*AP*GP*AP*UP*CP*UP *GP*CP*GP*GP*UP*CP*UP*GP*AP*GP*C)-3' | rna | 22 | — | — |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 2 copies
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 843 | 0.73 | 0.78 | 60 | empty |
| 2 | 258 | 0.73 | 0.87 | 29 | empty |
| 3 | 1009 | 0.73 | 0.76 | 64 | empty |
| 4 | 274 | 0.72 | 0.86 | 32 | empty |
| 5 | 170 | 0.56 | 0.81 | 24 | empty |
Interfaces
8 interfaces between chains.
- A–C · 883 Ų buried · 9 hydrogen bonds · protein-protein
- B–D · 805 Ų buried · 6 hydrogen bonds · protein-protein
- D–S · 531 Ų buried · 17 hydrogen bonds · protein-nucleic
- C–R · 525 Ų buried · 15 hydrogen bonds · protein-nucleic
- A–B · 214 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 2W2H · Structural basis of transcription activation by the Cyclin T1-Tat-TAR RNA complex from… · the same entry in another collection · chain S against S, TM-score 1.00
- Q9XT26 · AlphaFold monomer V2.0 prediction for cyclin-T1 (Q9XT26) · a predicted model of the same protein · chain B against A, TM-score 0.94
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 Q9XT26
- Every structure of UniProt P20920
- Elsewhere: RCSB PDB 2W2H · PDBe 2W2H · UniProt Q9XT26 · UniProt P20920
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