Research workbench
1.95 ångström resolution crystal structure of dsba disulfide interchange protein from klebsiella pneumoniae.
Analyse 1.95 ångström resolution crystal structure of dsba disulfide interchange… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6DXN
- Type
- protein
- Length
- 761 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- THIOL:DISULFIDE interchange protein
- UniProt
- A0A169B8J1
- Pockets
- 7 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 50% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D | THIOL:DISULFIDE interchange protein | protein | 191 | 50% helix, 10% strand | A0A169B8J1 |
| C | THIOL:DISULFIDE interchange protein | protein | 188 | 51% helix, 11% strand | A0A169B8J1 |
Ligands and binding sites
- PGE · Triethylene glycol · additive · 3 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 787 | 0.76 | 0.80 | 72 | empty |
| 2 | 574 | 0.65 | 0.76 | 56 | PGE |
| 3 | 216 | 0.55 | 0.79 | 35 | empty |
| 4 | 122 | 0.46 | 0.78 | 21 | empty |
| 5 | 161 | 0.43 | 0.74 | 23 | empty |
Interfaces
4 interfaces between chains.
- C–D · 715 Ų buried · 21 hydrogen bonds · protein-protein
- A–B · 499 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 219 Ų buried · 2 hydrogen bonds · protein-protein
- B–D · 194 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 24 modified (engineered).
Compared structures
- 6DXN · 1.95 Angstrom Resolution Crystal Structure of DsbA Disulfide Interchange Protein from… · 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 A0A169B8J1
- Elsewhere: RCSB PDB 6DXN · PDBe 6DXN · UniProt A0A169B8J1
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