MolNFT v1 · #94814 · protein
Dihydrodipicolinate synthase of agrobacterium tumefaciens
4I7U: “Dihydrodipicolinate synthase of agrobacterium tumefaciens”. X-ray diffraction, 12 pockets (best druggability 0.75). MolNFT v1 #94814 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4I7U
- Type
- protein
- Length
- 1,188 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dihydrodipicolinate synthase
- EC
- 4.2.1.52
- UniProt
- F0L8Z6
- Pockets
- 12 · best druggability 0.75
Structure
x-ray diffraction · 3 distinct chains · 51% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dihydrodipicolinate synthase (EC 4.2.1.52) | protein | 294 | 52% helix, 13% strand | F0L8Z6 |
| B | Dihydrodipicolinate synthase (EC 4.2.1.52) | protein | 304 | 50% helix, 12% strand | F0L8Z6 |
| C, D | Dihydrodipicolinate synthase (EC 4.2.1.52) | protein | 295 | 52% helix, 13% strand | F0L8Z6 |
Ligands and binding sites
- GOL · Glycerol · additive · 8 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 352 | 0.75 | 0.86 | 56 | empty |
| 2 | 391 | 0.75 | 0.86 | 61 | empty |
| 3 | 361 | 0.65 | 0.79 | 48 | GOL |
| 4 | 306 | 0.64 | 0.80 | 41 | empty |
| 5 | 305 | 0.62 | 0.79 | 40 | GOL |
Interfaces
4 interfaces between chains.
- C–D · 1482 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 1456 Ų buried · 19 hydrogen bonds · protein-protein
- A–D · 972 Ų buried · 14 hydrogen bonds · protein-protein
- B–C · 950 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 4I7U · Dihydrodipicolinate Synthase of Agrobacterium tumefaciens · 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 F0L8Z6
- Elsewhere: RCSB PDB 4I7U · PDBe 4I7U · UniProt F0L8Z6
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.