Research workbench
Crystal structure of the rice topless related protein 2 (TPR2) N- terminal topless domain (1-209) in complex with rice D53 repressor ear peptide motif
Analyse Crystal structure of the rice topless related protein 2 (TPR2) N- terminal… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5J9K
- Type
- protein
- Length
- 425 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein TPR1; Rice D53 peptide 794-808
- UniProt
- Q5NBT9
- Ligands
- ZN
- Pockets
- 4 · best druggability 0.51
Structure
x-ray diffraction · 4 distinct chains · 59% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein TPR1 | protein | 205 | 61% helix, 0% strand | Q5NBT9 |
| B | Protein TPR1 | protein | 203 | 62% helix, 0% strand | Q5NBT9 |
| C | Rice D53 peptide 794-808 | protein | 9 | 0% helix, 0% strand | — |
| D | Rice D53 peptide 794-808 | protein | 8 | 0% helix, 0% strand | — |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 150 | 0.51 | 0.79 | 20 | empty |
| 2 | 113 | 0.42 | 0.76 | 15 | empty |
| 3 | 61 | 0.33 | 0.76 | 14 | empty |
| 4 | 57 | 0.30 | 0.75 | 13 | empty |
Interfaces
3 interfaces between chains.
- A–B · 659 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 413 Ų buried · 6 hydrogen bonds · protein-protein
- B–D · 382 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 5J9K · Crystal structure of the rice Topless related protein 2 (TPR2) N-terminal topless domain… · the same entry in another collection · chain A against A, TM-score 1.00
- Q5NBT9 · AlphaFold monomer V2.0 prediction for protein TPR1 (Q5NBT9) · a predicted model of the same protein · chain B against A, TM-score 0.92
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 Q5NBT9
- Elsewhere: RCSB PDB 5J9K · PDBe 5J9K · UniProt Q5NBT9
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