Research workbench
Crystal structure of a trap periplasmic solute binding protein from desulfovibrio desulfuricans (DDES_1525), target efi-510107, with bound sn-glycerol-3-phosphate
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
- 4NHB
- Type
- protein
- Length
- 605 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Trap dicarboxylate transporter-dctp subunit
- UniProt
- B8J100
- Ligands
- G3P, IOD
- Pockets
- 7 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 52% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Trap dicarboxylate transporter-dctp subunit | protein | 294 | 53% helix, 19% strand | B8J100 |
| B | Trap dicarboxylate transporter-dctp subunit | protein | 311 | 51% helix, 18% strand | B8J100 |
Ligands and binding sites
- G3P · Sn-glycerol-3-phosphate · ligand · 2 copies · chains A, B
- IOD · Iodide ion · ion · 23 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1130 | 0.72 | 0.76 | 83 | IOD |
| 2 | 198 | 0.62 | 0.83 | 37 | G3P |
| 3 | 96 | 0.56 | 0.85 | 30 | G3P |
| 4 | 99 | 0.42 | 0.77 | 19 | empty |
| 5 | 98 | 0.36 | 0.75 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 892 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 4NHB · 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 B8J100
- Elsewhere: RCSB PDB 4NHB · PDBe 4NHB · UniProt B8J100
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