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Crystal structure of a FIMH*DSF complex from E.COLI K12 with bound heptyl alpha-D-mannopyrannoside

Analyse Crystal structure of a FIMH*DSF complex from E.COLI K12 with bound heptyl… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4XOB
Type: protein
Length: 1,168 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Protein fimh; Fimf
UniProt: P08191, C9QSZ9
Ligands: KGM, SO4
Pockets: 5 · best druggability 0.87

Structure

x-ray diffraction · 2 distinct chains · 3% helix, 52% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C, E, G	Protein fimh	protein	279	3% helix, 52% strand	P08191
B, D, F, H	Fimf	protein	13	0% helix, 69% strand	C9QSZ9

Ligands and binding sites

KGM · heptyl alpha-D-mannopyranoside · ligand · 4 copies · chains A, C, E, G
SO4 · Sulfate ion · ion · 2 copies · chains A, G, C

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1075	0.87	0.88	129	empty
2	653	0.68	0.77	69	empty
3	592	0.67	0.77	50	empty
4	130	0.41	0.75	30	empty
5	55	0.36	0.79	15	KGM

Interfaces

12 interfaces between chains.

C–E · 1302 Å² buried · 8 hydrogen bonds · protein-protein
C–D · 1105 Å² buried · 28 hydrogen bonds · protein-protein
A–B · 1100 Å² buried · 33 hydrogen bonds · protein-protein
E–F · 1097 Å² buried · 30 hydrogen bonds · protein-protein
G–H · 1073 Å² buried · 32 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 6 disulfide (disulfide).

Compared structures

4XOB · Crystal structure of a FimH*DsF complex from E.coli K12 with bound heptyl… · the same entry in another collection · chain H against H, TM-score 1.00
P08191 · AlphaFold monomer V2.0 prediction for type 1 fimbrin D-mannose specific adhesin (P08191) · a predicted model of the same protein · chain C against A, TM-score 0.96

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 P08191
Every structure of UniProt C9QSZ9
Elsewhere: RCSB PDB 4XOB · PDBe 4XOB · UniProt P08191 · UniProt C9QSZ9

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