MolNFT v1 · #50340 · protein
Crystal structure of dihydrodipicolinate synthase from hahella chejuensis at 1.5A resolution
2RFG: “Crystal structure of dihydrodipicolinate synthase from hahella chejuensis at 1.5A resolution”. X-ray diffraction, 1 ligand (MG), 11 pockets (best druggability 0.72). MolNFT v1 #50340 on GenesisL1: 3D structure, binding sites and…
- PDB
- 2RFG
- Type
- protein
- Length
- 1,164 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dihydrodipicolinate synthase
- EC
- 4.2.1.52
- UniProt
- Q2S9K4
- Ligands
- MG
- Pockets
- 11 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 51% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D | Dihydrodipicolinate synthase (EC 4.2.1.52) | protein | 289 | 51% helix, 13% strand | Q2S9K4 |
| B | Dihydrodipicolinate synthase (EC 4.2.1.52) | protein | 297 | 51% helix, 13% strand | Q2S9K4 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 303 | 0.72 | 0.85 | 58 | empty |
| 2 | 285 | 0.72 | 0.86 | 51 | empty |
| 3 | 288 | 0.63 | 0.80 | 42 | empty |
| 4 | 225 | 0.61 | 0.81 | 33 | empty |
| 5 | 285 | 0.59 | 0.78 | 46 | empty |
Interfaces
4 interfaces between chains.
- A–D · 1491 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 1484 Ų buried · 7 hydrogen bonds · protein-protein
- C–D · 883 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 822 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 2RFG · Crystal structure of dihydrodipicolinate synthase from Hahella chejuensis at 1.5A… · 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 Q2S9K4
- Elsewhere: RCSB PDB 2RFG · PDBe 2RFG · UniProt Q2S9K4
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