Research workbench
Crystal structure of the rice topless related protein 2 (TPR2) N- terminal domain (1-209) in complex with arabidopsis IAA1 peptide
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
- 5C7F
- Type
- protein
- Length
- 825 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ASPR2 protein; Auxin-responsive protein IAA1
- UniProt
- Q5NBT9, P49677
- Ligands
- ZN
- Pockets
- 13 · best druggability 0.42
Structure
x-ray diffraction · 7 distinct chains · 62% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ASPR2 protein | protein | 196 | 64% helix, 0% strand | Q5NBT9 |
| B | ASPR2 protein | protein | 199 | 62% helix, 0% strand | Q5NBT9 |
| C | ASPR2 protein | protein | 197 | 67% helix, 0% strand | Q5NBT9 |
| D | ASPR2 protein | protein | 200 | 62% helix, 0% strand | Q5NBT9 |
| E | Auxin-responsive protein IAA1 | protein | 9 | 0% helix, 0% strand | P49677 |
| F, H | Auxin-responsive protein IAA1 | protein | 8 | 0% helix, 0% strand | P49677 |
| G | Auxin-responsive protein IAA1 | protein | 8 | 0% helix, 0% strand | P49677 |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 copies · chains A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 57 | 0.42 | 0.82 | 16 | empty |
| 2 | 56 | 0.40 | 0.81 | 16 | empty |
| 3 | 51 | 0.38 | 0.81 | 18 | empty |
| 4 | 81 | 0.35 | 0.76 | 19 | empty |
| 5 | 80 | 0.34 | 0.75 | 18 | empty |
Interfaces
8 interfaces between chains.
- C–D · 2066 Ų buried · 51 hydrogen bonds · protein-protein
- A–B · 1957 Ų buried · 52 hydrogen bonds · protein-protein
- A–C · 706 Ų buried · 5 hydrogen bonds · protein-protein
- B–D · 675 Ų buried · 5 hydrogen bonds · protein-protein
- C–G · 670 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- Q5NBT9 · AlphaFold monomer V2.0 prediction for protein TPR1 (Q5NBT9) · a predicted model of the same protein · chain C against A, TM-score 0.94
- P49677 · AlphaFold monomer V2.0 prediction for auxin-responsive protein IAA1 (P49677) · a predicted model of the same protein · chain F against A, TM-score 0.42
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
- Every structure of UniProt P49677
- Elsewhere: RCSB PDB 5C7F · PDBe 5C7F · UniProt Q5NBT9 · UniProt P49677
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