Research workbench
Dihydrodipicolinate synthase from the common grapevine with pyruvate and lysine
Analyse Dihydrodipicolinate synthase from the common grapevine with pyruvate and lysine in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4HNN
- Type
- protein
- Length
- 2,472 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dihydrodipicolinate synthase
- UniProt
- D7U7T8
- Ligands
- LYS
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · 3 distinct chains · 47% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, E, G | Dihydrodipicolinate synthase | protein | 307 | 48% helix, 14% strand | D7U7T8 |
| C, D, H | Dihydrodipicolinate synthase | protein | 308 | 47% helix, 14% strand | D7U7T8 |
| F | Dihydrodipicolinate synthase | protein | 320 | 46% helix, 14% strand | D7U7T8 |
Ligands and binding sites
- LYS · Lysine · ligand · 8 copies · chains A, B, C, D, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 378 | 0.79 | 0.88 | 56 | LYS |
| 2 | 208 | 0.76 | 0.92 | 32 | LYS |
| 3 | 251 | 0.76 | 0.90 | 39 | LYS |
| 4 | 193 | 0.76 | 0.92 | 33 | LYS |
| 5 | 125 | 0.73 | 0.93 | 24 | empty |
Interfaces
15 interfaces between chains.
- E–F · 1947 Ų buried · 28 hydrogen bonds · protein-protein
- G–H · 1918 Ų buried · 31 hydrogen bonds · protein-protein
- C–D · 1889 Ų buried · 31 hydrogen bonds · protein-protein
- A–B · 1837 Ų buried · 27 hydrogen bonds · protein-protein
- B–F · 1041 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 modified (nonstandard).
Compared structures
- 4HNN · Dihydrodipicolinate Synthase from the common grapevine with pyruvate and lysine · the same entry in another collection · chain B against B, 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 D7U7T8
- Elsewhere: RCSB PDB 4HNN · PDBe 4HNN · UniProt D7U7T8
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