Research workbench
High resolution structure of dsbb C41S by joint calculation with solid-state NMR and X-ray data
Analyse High resolution structure of dsbb C41S by joint calculation with solid-state… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2LTQ
- Type
- protein
- Length
- 1,162 residues
- Chains
- 6
- Method
- solid-state nmr
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Disulfide bond formation protein B; Fab fragment light chain; Fab fragment heavy chain
- UniProt
- P0A6M2
- Ligands
- UQ1
- Pockets
- 14 · best druggability 0.82
Structure
solid-state nmr · 4 distinct chains · 13% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Disulfide bond formation protein B | protein | 148 | 53% helix, 0% strand | P0A6M2 |
| B, E | Fab fragment light chain | protein | 218 | 6% helix, 41% strand | — |
| C | Fab fragment heavy chain | protein | 216 | 1% helix, 49% strand | — |
| F | Fab fragment heavy chain | protein | 214 | 4% helix, 48% strand | — |
Ligands and binding sites
- UQ1 · Ubiquinone-1 · ligand · 2 copies · chains A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1041 | 0.82 | 0.83 | 91 | UQ1 |
| 2 | 1051 | 0.78 | 0.80 | 83 | UQ1 |
| 3 | 768 | 0.67 | 0.75 | 72 | empty |
| 4 | 263 | 0.55 | 0.76 | 42 | empty |
| 5 | 55 | 0.53 | 0.89 | 18 | empty |
Interfaces
8 interfaces between chains.
- E–F · 1829 Ų buried · 16 hydrogen bonds · protein-protein
- B–C · 1716 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 386 Ų buried · 7 hydrogen bonds · protein-protein
- C–F · 341 Ų buried · 3 hydrogen bonds · protein-protein
- D–E · 318 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide (disulfide).
Compared structures
- 2LTQ · High resolution structure of DsbB C41S by joint calculation with solid-state NMR and… · the same entry in another collection · chain F against F, TM-score 1.00
- P0A6M2 · AlphaFold monomer V2.0 prediction for disulfide bond formation protein B (P0A6M2) · a predicted model of the same protein · chain A against A, TM-score 0.83
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 P0A6M2
- Elsewhere: RCSB PDB 2LTQ · PDBe 2LTQ · UniProt P0A6M2
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