Research workbench
Crystal structure of a trap periplasmic solute binding protein from polaromonas sp JS666 (BPRO_0088, target efi-510167) bound to D- erythronate
Analyse Crystal structure of a trap periplasmic solute binding protein from polaromonas… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4PDD
- Type
- protein
- Length
- 909 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Trap dicarboxylate transporter, dctp subunit
- UniProt
- Q12HD7
- Ligands
- EAX
- Pockets
- 6 · best druggability 0.85
Structure
x-ray diffraction · 1 distinct chain · 51% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Trap dicarboxylate transporter, dctp subunit | protein | 303 | 51% helix, 21% strand | Q12HD7 |
Ligands and binding sites
- EAX · (2R,3R)-2,3,4-trihydroxybutanoic acid · ligand · 3 copies · chains A, B, C
- MLA · Malonic acid · additive · 7 copies · chains A, C, B
- FMT · Formic acid · additive · 5 copies · chains A, C, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1015 | 0.85 | 0.86 | 98 | MLA, FMT |
| 2 | 409 | 0.64 | 0.78 | 55 | empty |
| 3 | 347 | 0.64 | 0.79 | 49 | MLA |
| 4 | 304 | 0.63 | 0.79 | 35 | empty |
| 5 | 61 | 0.39 | 0.80 | 18 | empty |
Interfaces
3 interfaces between chains.
- A–B · 743 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 737 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 731 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide, 3 modified (disulfide, cyclization).
Compared structures
- 4PDD · CRYSTAL STRUCTURE OF A TRAP PERIPLASMIC SOLUTE BINDING PROTEIN FROM POLAROMONAS SP JS666… · 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 Q12HD7
- Elsewhere: RCSB PDB 4PDD · PDBe 4PDD · UniProt Q12HD7
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