Research workbench
Structure, function, stability and knockout phenotype of dihydrodipicolinate synthase from streptococcus pneumoniae
Analyse Structure, function, stability and knockout phenotype of dihydrodipicolinate… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3VFL
- 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
- K
- Pockets
- 5 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 48% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dihydrodipicolinate synthase (EC 4.2.1.52) | protein | 308 | 48% helix, 13% strand | A5LD17 |
| B | Dihydrodipicolinate synthase (EC 4.2.1.52) | protein | 306 | 48% helix, 13% strand | A5LD17 |
Ligands and binding sites
- K · Potassium ion · metal · 4 copies · chains A, B
- GOL · Glycerol · additive · 4 copies · chains A, B
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 591 | 0.74 | 0.81 | 57 | K, GOL |
| 2 | 153 | 0.53 | 0.80 | 30 | MES |
| 3 | 131 | 0.51 | 0.80 | 24 | MES |
| 4 | 87 | 0.38 | 0.76 | 19 | empty |
| 5 | 74 | 0.36 | 0.77 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 1975 Ų buried · 28 hydrogen bonds · protein-protein
Compared structures
- 3VFL · Structure, Function, Stability and Knockout Phenotype of Dihydrodipicolinate Synthase… · 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 A5LD17
- Elsewhere: RCSB PDB 3VFL · PDBe 3VFL · UniProt A5LD17
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