Research workbench
Cryo-EM structure of medicago truncatula HISN5 protein
Analyse Cryo-EM structure of medicago truncatula HISN5 protein in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7OJ5
- Type
- protein
- Length
- 4,416 residues
- Chains
- 24
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Imidazoleglycerol-phosphate dehydratase
- EC
- 4.2.1.19
- UniProt
- I3SDM5
- Ligands
- MN
- Pockets
- 20 · best druggability 0.78
Structure
electron microscopy · 1 distinct chain · 36% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, V, W, X, Y | Imidazoleglycerol-phosphate dehydratase (EC 4.2.1.19) | protein | 184 | 36% helix, 34% strand | I3SDM5 |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 48 copies · chains A, J, W, B, I, N, C, F, Q, D, S, H, E, L, Y, T, G, X, M, O, V, R, K, P
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 834 | 0.78 | 0.81 | 77 | empty |
| 2 | 866 | 0.78 | 0.81 | 82 | empty |
| 3 | 1001 | 0.78 | 0.80 | 80 | empty |
| 4 | 1043 | 0.77 | 0.80 | 82 | empty |
| 5 | 1045 | 0.77 | 0.80 | 86 | empty |
Interfaces
60 interfaces between chains.
- H–Q · 767 Ų buried · 6 hydrogen bonds · protein-protein
- J–S · 766 Ų buried · 6 hydrogen bonds · protein-protein
- F–M · 765 Ų buried · 6 hydrogen bonds · protein-protein
- K–W · 765 Ų buried · 6 hydrogen bonds · protein-protein
- B–W · 765 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 7OJ5 · Cryo-EM structure of Medicago truncatula HISN5 protein · 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 I3SDM5
- Elsewhere: RCSB PDB 7OJ5 · PDBe 7OJ5 · UniProt I3SDM5
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