Research workbench
Crystal structure of medicago truncatula L-histidinol dehydrogenase in complex with imidazole
Analyse Crystal structure of medicago truncatula L-histidinol dehydrogenase in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5VLB
- Type
- protein
- Length
- 2,598 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histidinol dehydrogenase, chloroplastic
- EC
- 1.1.1.23
- UniProt
- G7IKX3
- Ligands
- ZN
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 3 distinct chains · 47% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Histidinol dehydrogenase, chloroplastic (EC 1.1.1.23) | protein | 434 | 48% helix, 17% strand | G7IKX3 |
| C | Histidinol dehydrogenase, chloroplastic (EC 1.1.1.23) | protein | 431 | 46% helix, 16% strand | G7IKX3 |
| D, E, F | Histidinol dehydrogenase, chloroplastic (EC 1.1.1.23) | protein | 433 | 48% helix, 17% strand | G7IKX3 |
Ligands and binding sites
- ZN · Zinc ion · metal · 6 copies · chains A, B, C, D, E, F
- IMD · Imidazole · additive · 6 copies · chains A, B, C, D, E, F
- PEG · Di(hydroxyethyl)ether · additive · 6 copies · chains A, B, C, D, E, F
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 | 394 | 0.86 | 0.94 | 40 | empty |
| 2 | 402 | 0.86 | 0.94 | 39 | empty |
| 3 | 394 | 0.85 | 0.94 | 41 | empty |
| 4 | 584 | 0.74 | 0.81 | 67 | IMD |
| 5 | 563 | 0.73 | 0.81 | 59 | IMD |
Interfaces
13 interfaces between chains.
- C–D · 5654 Ų buried · 83 hydrogen bonds · protein-protein
- E–F · 5611 Ų buried · 90 hydrogen bonds · protein-protein
- A–B · 5586 Ų buried · 92 hydrogen bonds · protein-protein
- B–C · 416 Ų buried · 4 hydrogen bonds · protein-protein
- A–F · 397 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 5VLB · Crystal Structure of Medicago truncatula L-Histidinol Dehydrogenase in Complex with… · 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 G7IKX3
- Elsewhere: RCSB PDB 5VLB · PDBe 5VLB · UniProt G7IKX3
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