Research workbench
Crystal structure of barley thioredoxin H isoform 1 crystallized using ammonium sulfate as precipitant
Analyse Crystal structure of barley thioredoxin H isoform 1 crystallized using ammonium… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2VM1
- Type
- protein
- Length
- 442 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thioredoxin H isoform 1.
- EC
- 1.8.1.9
- UniProt
- Q7XZK3
- Ligands
- SO4
- Pockets
- 6 · best druggability 0.37
Structure
x-ray diffraction · 3 distinct chains · 43% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Thioredoxin H isoform 1. (EC 1.8.1.9) | protein | 110 | 44% helix, 26% strand | Q7XZK3 |
| C | Thioredoxin H isoform 1. (EC 1.8.1.9) | protein | 113 | 41% helix, 24% strand | Q7XZK3 |
| D | Thioredoxin H isoform 1. (EC 1.8.1.9) | protein | 109 | 45% helix, 26% strand | Q7XZK3 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 4 copies · chains B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 66 | 0.37 | 0.78 | 12 | empty |
| 2 | 118 | 0.36 | 0.73 | 24 | empty |
| 3 | 77 | 0.32 | 0.74 | 21 | empty |
| 4 | 76 | 0.30 | 0.73 | 15 | empty |
| 5 | 50 | 0.28 | 0.76 | 16 | empty |
Interfaces
3 interfaces between chains.
- A–D · 469 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 456 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 156 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 2VM1 · Crystal structure of barley thioredoxin h isoform 1 crystallized using ammonium sulfate… · the same entry in another collection · chain A against A, TM-score 1.00
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 Q7XZK3
- Elsewhere: RCSB PDB 2VM1 · PDBe 2VM1 · UniProt Q7XZK3
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.