MolNFT v1 · #42134 · protein
Structural features of the complex between the dsbd N-terminal and the pilb N-terminal domains from neisseria meningitidis
2K9F · Thioredoxin: “Structural features of the complex between the dsbd N-terminal and the pilb N-terminal domains from neisseria…”. Solution nmr, 4 pockets (best druggability 0.64). MolNFT v1 #42134 on GenesisL1: 3D structure, binding…
- PDB
- 2K9F
- Type
- protein
- Length
- 272 residues
- Chains
- 2
- Method
- solution nmr
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thioredoxin; THIOL:DISULFIDE interchange protein dsbd
- EC
- 1.8.1.8
- UniProt
- Q9JWM8, Q9JYM0
- Pockets
- 4 · best druggability 0.64
Structure
solution nmr · 2 distinct chains · 19% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Thioredoxin | protein | 144 | 33% helix, 20% strand | Q9JWM8 |
| B | THIOL:DISULFIDE interchange protein dsbd (EC 1.8.1.8) | protein | 128 | 3% helix, 48% strand | Q9JYM0 |
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 211 | 0.64 | 0.83 | 29 | empty |
| 2 | 175 | 0.54 | 0.79 | 23 | empty |
| 3 | 71 | 0.41 | 0.79 | 16 | empty |
| 4 | 71 | 0.36 | 0.77 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 796 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 2K9F · Structural features of the complex between the DsbD N-terminal and the PilB N-terminal… · the same entry in another collection · chain B against B, TM-score 1.00
- Q9JWM8 · AlphaFold monomer V2.0 prediction for peptide methionine sulfoxide reductase MSRA/MSRB… · a predicted model of the same protein · chain A against A, TM-score 0.88
- Q9JYM0 · AlphaFold monomer V2.0 prediction for THIOL:DISULFIDE interchange protein dsbd (Q9JYM0) · a predicted model of the same protein · chain B against A, TM-score 0.83
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 Q9JWM8
- Every structure of UniProt Q9JYM0
- Elsewhere: RCSB PDB 2K9F · PDBe 2K9F · UniProt Q9JWM8 · UniProt Q9JYM0
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