Research workbench
Crystal structure of escherichia COLI dihydrodipicolinate synthase and propionate covalently bound to K161.
Analyse Crystal structure of escherichia COLI dihydrodipicolinate synthase and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6NVA
- Type
- protein
- Length
- 2,350 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 4-hydroxy-tetrahydrodipicolinate synthase
- EC
- 4.3.3.7
- UniProt
- A0A066Q637
- Ligands
- NA
- Pockets
- 20 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 47% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, H | 4-hydroxy-tetrahydrodipicolinate synthase (EC 4.3.3.7) | protein | 294 | 47% helix, 12% strand | A0A066Q637 |
| F, G | 4-hydroxy-tetrahydrodipicolinate synthase (EC 4.3.3.7) | protein | 293 | 46% helix, 12% strand | A0A066Q637 |
Ligands and binding sites
- NA · Sodium ion · metal · 2 copies · chains C, F
- GOL · Glycerol · additive · 7 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, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 478 | 0.77 | 0.85 | 60 | GOL |
| 2 | 461 | 0.76 | 0.85 | 57 | GOL |
| 3 | 465 | 0.75 | 0.84 | 59 | GOL |
| 4 | 448 | 0.74 | 0.84 | 62 | GOL |
| 5 | 355 | 0.53 | 0.74 | 46 | empty |
Interfaces
12 interfaces between chains.
- C–D · 1348 Ų buried · 10 hydrogen bonds · protein-protein
- G–H · 1345 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 1333 Ų buried · 12 hydrogen bonds · protein-protein
- E–F · 1325 Ų buried · 9 hydrogen bonds · protein-protein
- F–H · 573 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 modified (nonstandard).
Compared structures
- 6NVA · Crystal structure of Escherichia coli dihydrodipicolinate synthase and propionate… · 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 A0A066Q637
- Elsewhere: RCSB PDB 6NVA · PDBe 6NVA · UniProt A0A066Q637
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