Research workbench
Crystal structure of a trap periplasmic solute binding protein from desulfovibrio alaskensis G20 (DDE_1548), target efi-510103, with bound D-ala-D-ala
Analyse Crystal structure of a trap periplasmic solute binding protein from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4NGU
- Type
- protein
- Length
- 319 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Trap dicarboxylate transporter, dctp subunit
- UniProt
- Q311Q1
- Ligands
- CL, SO4
- Pockets
- 3 · best druggability 0.47
Structure
x-ray diffraction · 1 distinct chain · 52% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Trap dicarboxylate transporter, dctp subunit | protein | 319 | 52% helix, 17% strand | Q311Q1 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 155 | 0.47 | 0.77 | 18 | empty |
| 2 | 86 | 0.40 | 0.78 | 22 | empty |
| 3 | 57 | 0.29 | 0.75 | 14 | empty |
Modifications
Observed in the structure: 16 modified, 2 d-amino (engineered, D-amino acid).
Compared structures
- 4NGU · Crystal structure of a TRAP periplasmic solute binding protein from Desulfovibrio… · 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 Q311Q1
- Elsewhere: RCSB PDB 4NGU · PDBe 4NGU · UniProt Q311Q1
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.