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Crystal structure of ligand free open conformation of sulfoquinovosyl binding protein (sqbp) from agrobacterium tumefaciens
Analyse Crystal structure of ligand free open conformation of sulfoquinovosyl binding… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7NBZ
- Type
- protein
- Length
- 1,152 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sulfoquinovosyl binding protein
- UniProt
- A0A083ZKV5
- Pockets
- 8 · best druggability 0.77
Structure
x-ray diffraction · 3 distinct chains · 46% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Sulfoquinovosyl binding protein | protein | 377 | 45% helix, 16% strand | A0A083ZKV5 |
| B | Sulfoquinovosyl binding protein | protein | 385 | 47% helix, 17% strand | A0A083ZKV5 |
| C | Sulfoquinovosyl binding protein | protein | 390 | 46% helix, 18% strand | A0A083ZKV5 |
Ligands and binding sites
- ACT · Acetate ion · additive · 3 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 762 | 0.77 | 0.81 | 95 | empty |
| 2 | 440 | 0.61 | 0.75 | 47 | ACT |
| 3 | 431 | 0.60 | 0.75 | 46 | empty |
| 4 | 247 | 0.50 | 0.74 | 31 | empty |
| 5 | 134 | 0.46 | 0.77 | 23 | empty |
Interfaces
3 interfaces between chains.
- A–C · 351 Ų buried · 3 hydrogen bonds · protein-protein
- A–B · 325 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 162 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 7NBZ · Crystal structure of ligand free open conformation of sulfoquinovosyl binding protein… · 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 7NBZ · PDBe 7NBZ · UniProt A0A083ZKV5
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