MolNFT v1 · #146646 · protein
Crystal structure of neisseria meningitidis dsbd C-terminal domain in the oxidised form
6DNU · THIOL:DISULFIDE interchange protein dsbd: “Crystal structure of neisseria meningitidis dsbd C-terminal domain in the oxidised form”. X-ray diffraction, 2 pockets (best druggability 0.32). MolNFT v1 #146646 on GenesisL1: 3D…
- PDB
- 6DNU
- Type
- protein
- Length
- 233 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
- Pockets
- 2 · best druggability 0.32
Structure
x-ray diffraction · 2 distinct chains · 44% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | THIOL:DISULFIDE interchange protein dsbd (EC 1.8.1.8) | protein | 116 | 44% helix, 16% strand | C6S7X6 |
| B | THIOL:DISULFIDE interchange protein dsbd (EC 1.8.1.8) | protein | 117 | 44% helix, 15% strand | C6S7X6 |
Ligands and binding sites
- P6G · Hexaethylene glycol · additive · 6 copies · chains A, B
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 | 59 | 0.32 | 0.76 | 14 | P6G |
| 2 | 65 | 0.31 | 0.75 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 572 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide, 1 covalent (disulfide, additive adduct).
Compared structures
- 6DNU · Crystal Structure of Neisseria meningitidis DsbD c-terminal domain in the oxidised 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 6DNU · PDBe 6DNU · UniProt C6S7X6
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