Research workbench
Crystal structure of the rice topless related protein 2 (TPR2) N- terminal domain (1-209) in complex with arabidopsis ninja 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
- 5C6V
- Type
- protein
- Length
- 830 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ASPR2 protein; Afp homolog 2
- UniProt
- Q5NBT9, Q9SV55
- Pockets
- 10 · best druggability 0.49
Structure
x-ray diffraction · 4 distinct chains · 63% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | ASPR2 protein | protein | 202 | 63% helix, 0% strand | Q5NBT9 |
| C | ASPR2 protein | protein | 198 | 63% helix, 0% strand | Q5NBT9 |
| D | ASPR2 protein | protein | 200 | 64% helix, 0% strand | Q5NBT9 |
| E, F, G, H | Afp homolog 2 | protein | 7 | 0% helix, 0% strand | Q9SV55 |
Pockets
10 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 111 | 0.49 | 0.81 | 19 | empty |
| 2 | 146 | 0.49 | 0.78 | 19 | empty |
| 3 | 115 | 0.49 | 0.80 | 17 | empty |
| 4 | 135 | 0.47 | 0.78 | 20 | empty |
| 5 | 103 | 0.39 | 0.76 | 20 | empty |
Interfaces
8 interfaces between chains.
- A–B · 2003 Ų buried · 43 hydrogen bonds · protein-protein
- C–D · 1989 Ų buried · 50 hydrogen bonds · protein-protein
- A–C · 673 Ų buried · 4 hydrogen bonds · protein-protein
- B–D · 664 Ų buried · 4 hydrogen bonds · protein-protein
- C–G · 540 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 5C6V · Crystal structure of the rice Topless related protein 2 (TPR2) N-terminal domain (1-209)… · the same entry in another collection · chain H against H, TM-score 1.00
- 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
- Q9SV55 · AlphaFold monomer V2.0 prediction for afp homolog 2 (Q9SV55) · a predicted model of the same protein · chain E against A, TM-score 0.56
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 Q9SV55
- Elsewhere: RCSB PDB 5C6V · PDBe 5C6V · UniProt Q5NBT9 · UniProt Q9SV55
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