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Crystal structure of a marine metagenome trap solute binding protein specific for pyroglutamate (sorcerer II global ocean sampling expedition, unidentified microbe, SCF7180008839099) in complex with co-purified pyroglutamate

Analyse Crystal structure of a marine metagenome trap solute binding protein specific… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6WGM
Type: protein
Length: 304 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Trap-type C4-dicarboxylate transport system, periplasmic component
UniProt: G5ZWD6
Ligands: PCA, CL
Pockets: 1 · best druggability 0.52

Structure

x-ray diffraction · 1 distinct chain · 53% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Trap-type C4-dicarboxylate transport system, periplasmic component	protein	304	53% helix, 17% strand	G5ZWD6

Ligands and binding sites

PCA · Pyroglutamic acid · ligand · chains A
CL · Chloride ion · ion · chains A
FMT · Formic acid · additive · 10 copies · chains A
EDO · 1,2-ethanediol · additive · 6 copies · chains A

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	130	0.52	0.81	18	EDO

Compared structures

6WGM · Crystal structure of a marine metagenome TRAP solute binding protein specific for… · 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 G5ZWD6
Elsewhere: RCSB PDB 6WGM · PDBe 6WGM · UniProt G5ZWD6

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