MolNFT v1 · #116693 · protein

Crystal structure from a domain (THR161-F265) from fructose-specific iiabc component (pts system) from borrelia burgdorferi

5DLE · Pts system, fructose-specific iiabc component: “Crystal structure from a domain (THR161-F265) from fructose-specific iiabc component (pts system) from…”. X-ray diffraction, 1 ligand (CL), 3 pockets (best druggability 0.55). MolNFT…

PDB: 5DLE
Type: protein
Length: 416 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Pts system, fructose-specific iiabc component
UniProt: O51369
Ligands: CL
Pockets: 3 · best druggability 0.55

Structure

x-ray diffraction · 1 distinct chain · 38% helix, 27% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Pts system, fructose-specific iiabc component	protein	104	38% helix, 27% strand	O51369

Ligands and binding sites

CL · Chloride ion · ion · chains A, B
IMD · Imidazole · additive · 4 copies · chains A, B, C, D

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	152	0.55	0.81	29	empty
2	122	0.44	0.77	28	empty
3	71	0.33	0.76	16	empty

Interfaces

5 interfaces between chains.

B–C · 555 Å² buried · 6 hydrogen bonds · protein-protein
A–D · 544 Å² buried · 6 hydrogen bonds · protein-protein
A–C · 372 Å² buried · 3 hydrogen bonds · protein-protein
B–D · 370 Å² buried · 2 hydrogen bonds · protein-protein
A–B · 131 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

5DLE · Crystal structure from a domain (Thr161-F265) from fructose-specific iiabc component (Pts… · 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 O51369
Elsewhere: RCSB PDB 5DLE · PDBe 5DLE · UniProt O51369

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