Research workbench
Crystal structure of medicago truncatula L-histidinol dehydrogenase in complex with L-histidine and NAD+
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
- 5VLD
- Type
- protein
- Length
- 2,590 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
- HIS, NAD, ZN
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 6 distinct chains · 46% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Histidinol dehydrogenase, chloroplastic (EC 1.1.1.23) | protein | 430 | 46% helix, 17% strand | G7IKX3 |
| B | Histidinol dehydrogenase, chloroplastic (EC 1.1.1.23) | protein | 429 | 46% helix, 18% strand | G7IKX3 |
| C | Histidinol dehydrogenase, chloroplastic (EC 1.1.1.23) | protein | 431 | 46% helix, 17% strand | G7IKX3 |
| D | Histidinol dehydrogenase, chloroplastic (EC 1.1.1.23) | protein | 433 | 46% helix, 17% strand | G7IKX3 |
| E | Histidinol dehydrogenase, chloroplastic (EC 1.1.1.23) | protein | 432 | 46% helix, 17% strand | G7IKX3 |
| F | Histidinol dehydrogenase, chloroplastic (EC 1.1.1.23) | protein | 435 | 46% helix, 17% strand | G7IKX3 |
Ligands and binding sites
- HIS · Histidine · ligand · 6 copies · chains A, B, C, D, E, F
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 6 copies · chains A, B, C, D, E, F
- ZN · Zinc ion · metal · 6 copies · chains A, B, C, D, E, F
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains A, 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, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 394 | 0.86 | 0.94 | 50 | empty |
| 2 | 418 | 0.86 | 0.94 | 52 | empty |
| 3 | 390 | 0.85 | 0.94 | 37 | empty |
| 4 | 1105 | 0.74 | 0.77 | 113 | empty |
| 5 | 344 | 0.74 | 0.85 | 49 | HIS, NAD |
Interfaces
13 interfaces between chains.
- E–F · 5565 Ų buried · 102 hydrogen bonds · protein-protein
- C–D · 5558 Ų buried · 93 hydrogen bonds · protein-protein
- A–B · 5501 Ų buried · 93 hydrogen bonds · protein-protein
- B–C · 421 Ų buried · 5 hydrogen bonds · protein-protein
- A–F · 398 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 5VLD · 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 5VLD · PDBe 5VLD · UniProt G7IKX3
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