MolNFT v1 · #58470 · protein
Crystal structure of dihydrodipicolinate synthase from agrobacterium tumefaciens str. C58
3B4U: “Crystal structure of dihydrodipicolinate synthase from agrobacterium tumefaciens str. C58”. X-ray diffraction, 1 ligand (MG), 6 pockets (best druggability 0.74). MolNFT v1 #58470 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 3B4U
- Type
- protein
- Length
- 575 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dihydrodipicolinate synthase
- UniProt
- Q8UCI4
- Ligands
- MG
- Pockets
- 6 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 51% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dihydrodipicolinate synthase | protein | 287 | 51% helix, 14% strand | Q8UCI4 |
| B | Dihydrodipicolinate synthase | protein | 288 | 51% helix, 14% strand | Q8UCI4 |
Ligands and binding sites
- MG · Magnesium ion · metal · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 99 | 0.74 | 0.96 | 28 | empty |
| 2 | 368 | 0.70 | 0.82 | 44 | empty |
| 3 | 421 | 0.70 | 0.81 | 52 | empty |
| 4 | 127 | 0.50 | 0.80 | 19 | empty |
| 5 | 109 | 0.38 | 0.75 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 1640 Ų buried · 25 hydrogen bonds · protein-protein
Compared structures
- 3B4U · Crystal structure of dihydrodipicolinate synthase from Agrobacterium tumefaciens str. C58 · 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 Q8UCI4
- Elsewhere: RCSB PDB 3B4U · PDBe 3B4U · UniProt Q8UCI4
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