MolNFT v1 · #103330 · protein

Crystal structure of a trap periplasmic solute binding protein from polaromonas sp JS666 (BPRO_1871, target efi-510164) bound to D- erythronate

4PDH · Trap dicarboxylate transporter, dctp subunit: “Crystal structure of a trap periplasmic solute binding protein from polaromonas sp JS666 (BPRO_1871, target…”. X-ray diffraction, 1 ligand (EAX), 3 pockets (best druggability 0.30).…

PDB: 4PDH
Type: protein
Length: 301 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Trap dicarboxylate transporter, dctp subunit
UniProt: Q12CD8
Ligands: EAX
Pockets: 3 · best druggability 0.30

Structure

x-ray diffraction · 1 distinct chain · 51% helix, 22% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Trap dicarboxylate transporter, dctp subunit	protein	301	51% helix, 22% strand	Q12CD8

Ligands and binding sites

EAX · (2R,3R)-2,3,4-trihydroxybutanoic acid · ligand · chains A

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.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	75	0.30	0.73	13	empty
2	53	0.29	0.75	12	empty
3	54	0.28	0.75	13	empty

Modifications

Observed in the structure: 1 modified (cyclization).

Compared structures

4PDH · 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 Q12CD8
Elsewhere: RCSB PDB 4PDH · PDBe 4PDH · UniProt Q12CD8

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.