Research workbench
Structure of dihydrodipicolinate synthase from streptococcus PNEUMONIAE,BOUND to pyruvate and lysine
Analyse Structure of dihydrodipicolinate synthase from streptococcus PNEUMONIAE,BOUND… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4FHA
- Type
- protein
- Length
- 614 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dihydrodipicolinate synthase
- EC
- 4.2.1.52
- UniProt
- A5LD17
- Ligands
- LYS, NA
- Pockets
- 5 · best druggability 0.73
Structure
x-ray diffraction · 1 distinct chain · 49% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Dihydrodipicolinate synthase (EC 4.2.1.52) | protein | 307 | 49% helix, 13% strand | A5LD17 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 400 | 0.73 | 0.84 | 51 | LYS |
| 2 | 140 | 0.48 | 0.78 | 24 | empty |
| 3 | 112 | 0.42 | 0.76 | 22 | empty |
| 4 | 79 | 0.38 | 0.77 | 20 | empty |
| 5 | 70 | 0.35 | 0.77 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 1953 Ų buried · 21 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (nonstandard).
Compared structures
- 4FHA · Structure of Dihydrodipicolinate Synthase from Streptococcus pneumoniae,bound to pyruvate… · 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 A5LD17
- Elsewhere: RCSB PDB 4FHA · PDBe 4FHA · UniProt A5LD17
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