Research workbench
Crystal structure of the escherichia COLI twin arginine leader peptide binding protein dmsd in a monomeric form
Analyse Crystal structure of the escherichia COLI twin arginine leader peptide binding… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3EFP
- Type
- protein
- Length
- 412 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Twin-arginine leader-binding protein dmsd
- UniProt
- P69853
- Ligands
- NA, CL
- Pockets
- 2 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 59% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Twin-arginine leader-binding protein dmsd | protein | 204 | 60% helix, 1% strand | P69853 |
| B | Twin-arginine leader-binding protein dmsd | protein | 208 | 58% helix, 1% strand | P69853 |
Ligands and binding sites
- NA · Sodium ion · metal · chains B
- CL · Chloride ion · ion · 6 copies · chains A, B
- GOL · Glycerol · additive · 6 copies · chains A, B
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · 4 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1035 | 0.79 | 0.80 | 78 | empty |
| 2 | 65 | 0.35 | 0.77 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 617 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 3EFP · Crystal structure of the Escherichia coli twin arginine leader peptide binding protein… · the same entry in another collection · chain A against A, TM-score 1.00
- P69853 · AlphaFold monomer V2.0 prediction for tat proofreading chaperone dmsd (P69853) · a predicted model of the same protein · chain A 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 P69853
- Elsewhere: RCSB PDB 3EFP · PDBe 3EFP · UniProt P69853
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