MolNFT v1 · #123116 · protein
Crystal structure of the rice topless related protein 2 (TPR2) N- terminal topless domain (1-209) L111A and L130A mutant in complex with rice D53 repressor ear peptide motif
5JA5 · Protein TPR1: “Crystal structure of the rice topless related protein 2 (TPR2) N- terminal topless domain (1-209) L111A and…”. X-ray diffraction, 1 ligand (ZN), 2 pockets (best druggability 0.61). MolNFT v1 #123116 on GenesisL1: 3D…
- PDB
- 5JA5
- Type
- protein
- Length
- 208 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein TPR1; The rice D53 peptide (A.A. 794-808)
- UniProt
- Q5NBT9
- Ligands
- ZN
- Pockets
- 2 · best druggability 0.61
Structure
x-ray diffraction · 2 distinct chains · 62% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein TPR1 | protein | 201 | 64% helix, 0% strand | Q5NBT9 |
| B | The rice D53 peptide (A.A. 794-808) | protein | 7 | 0% helix, 0% strand | — |
Ligands and binding sites
- ZN · Zinc ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 267 | 0.61 | 0.79 | 27 | empty |
| 2 | 51 | 0.28 | 0.74 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 430 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 5JA5 · 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 A 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 5JA5 · PDBe 5JA5 · UniProt Q5NBT9
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