Research workbench
Crystal structure of neisseria meningitidis dsbd N-terminal domain in the reduced form
Analyse Crystal structure of neisseria meningitidis dsbd N-terminal domain in the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6DNV
- Type
- protein
- Length
- 248 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- THIOL:DISULFIDE interchange protein dsbd
- EC
- 1.8.1.8
- UniProt
- C6S7X6
- Ligands
- SO4
- Pockets
- 2 · best druggability 0.40
Structure
x-ray diffraction · 2 distinct chains · 7% helix, 56% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | THIOL:DISULFIDE interchange protein dsbd (EC 1.8.1.8) | protein | 123 | 6% helix, 56% strand | C6S7X6 |
| B | THIOL:DISULFIDE interchange protein dsbd (EC 1.8.1.8) | protein | 125 | 8% helix, 57% strand | C6S7X6 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 133 | 0.40 | 0.74 | 28 | empty |
| 2 | 130 | 0.40 | 0.74 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 632 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 6DNV · Crystal Structure of Neisseria meningitidis DsbD n-terminal domain in the reduced form · 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 C6S7X6
- Elsewhere: RCSB PDB 6DNV · PDBe 6DNV · UniProt C6S7X6
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