Research workbench
Crystal structure of a trap periplasmic solute binding protein from chromohalobacter salexigens dsm 3043 (CSAL_0660), target efi-501075, with bound D-alanine-D-alanine
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
- 4N8G
- Type
- protein
- Length
- 1,282 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Trap dicarboxylate transporter, dctp subunit
- UniProt
- Q1QZT7
- Ligands
- CL, SO4
- Pockets
- 10 · best druggability 0.84
Structure
x-ray diffraction · 4 distinct chains · 52% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Trap dicarboxylate transporter, dctp subunit | protein | 327 | 53% helix, 16% strand | Q1QZT7 |
| B | Trap dicarboxylate transporter, dctp subunit | protein | 323 | 52% helix, 15% strand | Q1QZT7 |
| C | Trap dicarboxylate transporter, dctp subunit | protein | 318 | 53% helix, 16% strand | Q1QZT7 |
| D | Trap dicarboxylate transporter, dctp subunit | protein | 314 | 52% helix, 16% strand | Q1QZT7 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 536 | 0.84 | 0.90 | 81 | empty |
| 2 | 598 | 0.84 | 0.89 | 97 | empty |
| 3 | 778 | 0.75 | 0.80 | 66 | empty |
| 4 | 361 | 0.69 | 0.82 | 37 | empty |
| 5 | 311 | 0.69 | 0.83 | 32 | empty |
Interfaces
4 interfaces between chains.
- C–D · 1242 Ų buried · 21 hydrogen bonds · protein-protein
- A–B · 1153 Ų buried · 23 hydrogen bonds · protein-protein
- A–C · 866 Ų buried · 18 hydrogen bonds · protein-protein
- B–D · 857 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 36 modified, 8 d-amino (engineered, D-amino acid).
Compared structures
- 4N8G · Crystal structure of a TRAP periplasmic solute binding protein from Chromohalobacter… · 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 Q1QZT7
- Elsewhere: RCSB PDB 4N8G · PDBe 4N8G · UniProt Q1QZT7
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