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Dihydrodipicolinate synthase (dhdps) from C.JEJUNI, with pyruvate bound in the active site and L-lysine bound at the allosteric site in C121 space group
Analyse Dihydrodipicolinate synthase (dhdps) from C.JEJUNI, with pyruvate bound in the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7LCF
- Type
- protein
- Length
- 3,553 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 4-hydroxy-tetrahydrodipicolinate synthase
- EC
- 4.3.3.7
- UniProt
- Q9PPB4
- Ligands
- LYS, MG
- Pockets
- 20 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 46% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 4-hydroxy-tetrahydrodipicolinate synthase (EC 4.3.3.7) | protein | 297 | 46% helix, 14% strand | Q9PPB4 |
| B, C, D, E, F, G, H, I, J, K, L | 4-hydroxy-tetrahydrodipicolinate synthase (EC 4.3.3.7) | protein | 296 | 46% helix, 14% strand | Q9PPB4 |
Ligands and binding sites
- LYS · Lysine · ligand · 12 copies · chains A, G, B, F, C, L, D, I, E, K, H, J
- MG · Magnesium ion · metal · chains 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, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 242 | 0.73 | 0.88 | 39 | LYS |
| 2 | 836 | 0.70 | 0.76 | 67 | empty |
| 3 | 200 | 0.69 | 0.87 | 27 | LYS |
| 4 | 189 | 0.69 | 0.87 | 26 | LYS |
| 5 | 188 | 0.68 | 0.87 | 26 | LYS |
Interfaces
15 interfaces between chains.
- H–J · 1505 Ų buried · 15 hydrogen bonds · protein-protein
- D–I · 1500 Ų buried · 15 hydrogen bonds · protein-protein
- E–K · 1495 Ų buried · 16 hydrogen bonds · protein-protein
- B–F · 1490 Ų buried · 16 hydrogen bonds · protein-protein
- A–G · 1471 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 modified (nonstandard).
Compared structures
- 7LCF · Dihydrodipicolinate synthase (DHDPS) from C.jejuni, with pyruvate bound in the active… · the same entry in another collection · chain L against L, 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 Q9PPB4
- Elsewhere: RCSB PDB 7LCF · PDBe 7LCF · UniProt Q9PPB4
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