MolNFT v1 · #25448 · protein
Crystal structure of the disulfide-linked complex between the N- terminal and C-terminal domain of the electron transfer catalyst dsbd
1VRS · THIOL:DISULFIDE interchange protein dsbd: “Crystal structure of the disulfide-linked complex between the N- terminal and C-terminal domain of the…”. X-ray diffraction, 9 pockets (best druggability 0.53). MolNFT v1 #25448 on…
- PDB
- 1VRS
- Type
- protein
- Length
- 713 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- THIOL:DISULFIDE interchange protein dsbd
- EC
- 1.8.1.8
- UniProt
- P36655
- Pockets
- 9 · best druggability 0.53
Structure
x-ray diffraction · 5 distinct chains · 19% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | THIOL:DISULFIDE interchange protein dsbd (EC 1.8.1.8) | protein | 121 | 6% helix, 60% strand | P36655 |
| D, F | THIOL:DISULFIDE interchange protein dsbd (EC 1.8.1.8) | protein | 118 | 39% helix, 19% strand | P36655 |
| B | THIOL:DISULFIDE interchange protein dsbd (EC 1.8.1.8) | protein | 125 | 6% helix, 57% strand | P36655 |
| E | THIOL:DISULFIDE interchange protein dsbd (EC 1.8.1.8) | protein | 118 | 40% helix, 19% strand | P36655 |
| C | THIOL:DISULFIDE interchange protein dsbd (EC 1.8.1.8) | protein | 113 | 6% helix, 64% strand | P36655 |
Pockets
9 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 251 | 0.53 | 0.76 | 32 | empty |
| 2 | 98 | 0.49 | 0.81 | 25 | empty |
| 3 | 92 | 0.47 | 0.81 | 25 | empty |
| 4 | 108 | 0.46 | 0.79 | 21 | empty |
| 5 | 84 | 0.42 | 0.79 | 17 | empty |
Interfaces
6 interfaces between chains.
- A–D · 977 Ų buried · 12 hydrogen bonds · protein-protein
- B–E · 930 Ų buried · 9 hydrogen bonds · protein-protein
- C–F · 689 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 237 Ų buried · 1 hydrogen bond · protein-protein
- D–C · 103 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 1VRS · Crystal structure of the disulfide-linked complex between the N-terminal and C-terminal… · 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 F against A, TM-score 0.98
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
- Elsewhere: RCSB PDB 1VRS · PDBe 1VRS · UniProt P36655
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