Research workbench
Crystal structure of dihydrodipicolinate synthase from rhodopseudomonas palustris at 2.0A resolution
Analyse Crystal structure of dihydrodipicolinate synthase from rhodopseudomonas… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3EB2
- Type
- protein
- Length
- 1,157 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative dihydrodipicolinate synthetase
- EC
- 4.2.1.52
- UniProt
- Q6N9H8
- Pockets
- 16 · best druggability 0.78
Structure
x-ray diffraction · 3 distinct chains · 51% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Putative dihydrodipicolinate synthetase (EC 4.2.1.52) | protein | 288 | 51% helix, 15% strand | Q6N9H8 |
| B | Putative dihydrodipicolinate synthetase (EC 4.2.1.52) | protein | 291 | 51% helix, 14% strand | Q6N9H8 |
| D | Putative dihydrodipicolinate synthetase (EC 4.2.1.52) | protein | 290 | 50% helix, 14% strand | Q6N9H8 |
Ligands and binding sites
- PGE · Triethylene glycol · additive · 2 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 587 | 0.78 | 0.84 | 77 | empty |
| 2 | 548 | 0.77 | 0.84 | 75 | empty |
| 3 | 67 | 0.72 | 0.97 | 19 | empty |
| 4 | 57 | 0.72 | 0.98 | 18 | empty |
| 5 | 54 | 0.71 | 0.98 | 18 | empty |
Interfaces
4 interfaces between chains.
- B–D · 1309 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 1303 Ų buried · 10 hydrogen bonds · protein-protein
- C–D · 1106 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 1085 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 3EB2 · Crystal structure of Dihydrodipicolinate Synthase from Rhodopseudomonas palustris at 2.0A… · 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 Q6N9H8
- Elsewhere: RCSB PDB 3EB2 · PDBe 3EB2 · UniProt Q6N9H8
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