Research workbench
Crystal structure of the disulfide-linked complex between the N- terminal domain of the electron transfer catalyst dsbd and the cytochrome C biogenesis protein ccmg
Analyse Crystal structure of the disulfide-linked complex between the N- terminal… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1Z5Y
- Type
- protein
- Length
- 254 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- THIOL:DISULFIDE interchange protein dsbd; THIOL:DISULFIDE interchange protein dsbe
- EC
- 1.8.1.8
- UniProt
- P36655, P0AA86
- Ligands
- CL
- Pockets
- 4 · best druggability 0.41
Structure
x-ray diffraction · 2 distinct chains · 24% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D | THIOL:DISULFIDE interchange protein dsbd (EC 1.8.1.8) | protein | 118 | 6% helix, 62% strand | P36655 |
| E | THIOL:DISULFIDE interchange protein dsbe | protein | 136 | 40% helix, 25% strand | P0AA86 |
Ligands and binding sites
- CL · Chloride ion · ion · 3 copies · chains D, E
- EDO · 1,2-ethanediol · additive · 4 copies · chains D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 86 | 0.41 | 0.77 | 16 | empty |
| 2 | 55 | 0.33 | 0.77 | 19 | EDO |
| 3 | 57 | 0.32 | 0.76 | 12 | EDO |
| 4 | 51 | 0.28 | 0.75 | 18 | empty |
Interfaces
1 interface between chains.
- D–E · 707 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 1Z5Y · Crystal Structure Of The Disulfide-Linked Complex Between The N-Terminal Domain Of The… · the same entry in another collection · chain D against D, TM-score 1.00
- P36655 · AlphaFold monomer V2.0 prediction for THIOL:DISULFIDE interchange protein dsbd (P36655) · a predicted model of the same protein · chain D against A, TM-score 0.97
- P0AA86 · AlphaFold monomer V2.0 prediction for THIOL:DISULFIDE interchange protein dsbe (P0AA86) · a predicted model of the same protein · chain E against A, TM-score 0.97
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 P36655
- Every structure of UniProt P0AA86
- Elsewhere: RCSB PDB 1Z5Y · PDBe 1Z5Y · UniProt P36655 · UniProt P0AA86
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