Research workbench
Structure of the sbsb S-layer protein of geobacillus stearothermophilus PV72P2 in complex with nanobody KB6
Analyse Structure of the sbsb S-layer protein of geobacillus stearothermophilus PV72P2… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4AQ1
- Type
- protein
- Length
- 1,596 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sbsb protein; NBKB6
- UniProt
- Q45664
- Ligands
- CA
- Pockets
- 13 · best druggability 0.77
Structure
x-ray diffraction · 3 distinct chains · 5% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Sbsb protein | protein | 721 | 5% helix, 46% strand | Q45664 |
| B, D | NBKB6 | protein | 124 | 7% helix, 51% strand | — |
| C | Sbsb protein | protein | 627 | 5% helix, 45% strand | Q45664 |
Ligands and binding sites
- CA · Calcium ion · metal · 8 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1067 | 0.77 | 0.79 | 122 | empty |
| 2 | 620 | 0.71 | 0.79 | 47 | empty |
| 3 | 504 | 0.68 | 0.79 | 76 | empty |
| 4 | 101 | 0.55 | 0.85 | 33 | empty |
| 5 | 187 | 0.47 | 0.75 | 32 | empty |
Interfaces
4 interfaces between chains.
- C–D · 451 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 407 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 194 Ų buried · 4 hydrogen bonds · protein-protein
- A–D · 21 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 4AQ1 · Structure of the SbsB S-layer protein of Geobacillus stearothermophilus PV72p2 in complex… · 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 Q45664
- Elsewhere: RCSB PDB 4AQ1 · PDBe 4AQ1 · UniProt Q45664
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