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Crystal structure of the pbp soca from agrobacterium tumefaciens C58 in complex with dfg at 1.5 a resolution
Analyse Crystal structure of the pbp soca from agrobacterium tumefaciens C58 in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5LOM
- Type
- protein
- Length
- 491 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Deoxyfructosyl-amino acid transporter periplasmic binding protein
- UniProt
- Q7D447
- Ligands
- SNW
- Pockets
- 6 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 36% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Deoxyfructosyl-amino acid transporter periplasmic binding protein | protein | 241 | 37% helix, 22% strand | Q7D447 |
| B | Deoxyfructosyl-amino acid transporter periplasmic binding protein | protein | 250 | 36% helix, 22% strand | Q7D447 |
Ligands and binding sites
- SNW · Deoxyfructosylglutamine · ligand · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 3 copies · 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 174 | 0.77 | 0.93 | 42 | SNW |
| 2 | 175 | 0.77 | 0.93 | 44 | SNW |
| 3 | 490 | 0.69 | 0.79 | 52 | empty |
| 4 | 53 | 0.30 | 0.75 | 12 | empty |
| 5 | 52 | 0.27 | 0.74 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 459 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 5LOM · Crystal structure of the PBP SocA from Agrobacterium tumefaciens C58 in complex with DFG… · 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 Q7D447
- Elsewhere: RCSB PDB 5LOM · PDBe 5LOM · UniProt Q7D447
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