Research workbench
Crystal structure of sq binding protein from agrobacterium tumefaciens in complex with sulfoquinovosyl glycerol (sqgro)
Analyse Crystal structure of sq binding protein from agrobacterium tumefaciens in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7OFY
- Type
- protein
- Length
- 777 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sulfoquinovosyl binding protein
- UniProt
- A0A083ZKV5
- Ligands
- VCW
- Pockets
- 5 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 47% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Sulfoquinovosyl binding protein | protein | 389 | 46% helix, 18% strand | A0A083ZKV5 |
| B | Sulfoquinovosyl binding protein | protein | 388 | 47% helix, 18% strand | A0A083ZKV5 |
Ligands and binding sites
- VCW · [(2S,3S,4S,5R,6S)-6-[(2R)-2,3-bis(oxidanyl)propoxy]-3, 4,5-tris(oxidanyl)oxan-2-yl]methanesulfonic acid · ligand · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 10 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 939 | 0.81 | 0.83 | 94 | EDO |
| 2 | 99 | 0.78 | 0.98 | 25 | VCW |
| 3 | 95 | 0.78 | 0.98 | 23 | VCW |
| 4 | 131 | 0.49 | 0.79 | 25 | empty |
| 5 | 87 | 0.46 | 0.81 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 893 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 7OFY · Crystal structure of SQ binding protein from Agrobacterium tumefaciens in complex with… · 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 A0A083ZKV5
- Elsewhere: RCSB PDB 7OFY · PDBe 7OFY · UniProt A0A083ZKV5
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