MolNFT v1 · #100817 · protein

Crystal structure of a trap periplasmic solute binding protein from bradyrhizobium sp. BTAI1 B (BBTA_0128), target efi-510056 (BBTA_0128), complex with ALPHA/BETA-D-galacturonate

4N8Y · Putative trap-type C4-dicarboxylate transport system…: “Crystal structure of a trap periplasmic solute binding protein from bradyrhizobium sp. BTAI1 B (BBTA_0128)…”. X-ray diffraction, 2 ligands (GTR, ADA), 3 pockets (best…

PDB: 4N8Y
Type: protein
Length: 600 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Putative trap-type C4-dicarboxylate transport system, binding periplasmic protein (dctp…
UniProt: A5E8D2
Ligands: GTR, ADA
Pockets: 3 · best druggability 0.77

Structure

x-ray diffraction · 1 distinct chain · 51% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Putative trap-type C4-dicarboxylate transport system, binding periplasmic protein (dctp subunit)	protein	300	51% helix, 19% strand	A5E8D2

Ligands and binding sites

GTR · beta-D-galactopyranuronic acid · ligand · 2 copies · chains A, B
ADA · alpha-D-galactopyranuronic acid · sugar · 2 copies · chains A, B

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

Pockets

3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	650	0.77	0.83	75	ADA, GTR
2	51	0.67	0.97	20	ADA, GTR
3	56	0.29	0.75	23	empty

Interfaces

1 interface between chains.

A–B · 858 Å² buried · 12 hydrogen bonds · protein-protein

Compared structures

4N8Y · Crystal structure of a trap periplasmic solute binding protein from bradyrhizobium sp.… · 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 A5E8D2
Elsewhere: RCSB PDB 4N8Y · PDBe 4N8Y · UniProt A5E8D2

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