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Crystal structure of the fimd usher bound to its cognate FIMC:FIMH substrate

Analyse Crystal structure of the fimd usher bound to its cognate FIMC:FIMH substrate in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3RFZ
Type: protein
Length: 2,516 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Type 1 fimbrial adhesin; Outer membrane usher protein, type 1 fimbrial synthesis…
UniProt: Q5D223, C6UL88, P59590
Ligands: SO4
Pockets: 20 · best druggability 0.90

Structure

x-ray diffraction · 4 distinct chains · 6% helix, 54% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, D	Type 1 fimbrial adhesin	protein	279	2% helix, 51% strand	Q5D223
B	Outer membrane usher protein, type 1 fimbrial synthesis	protein	778	6% helix, 55% strand	C6UL88
C, F	Chaperone protein fimc	protein	201	3% helix, 52% strand	P59590
E	Outer membrane usher protein, type 1 fimbrial synthesis	protein	778	7% helix, 54% strand	C6UL88

Ligands and binding sites

SO4 · Sulfate ion · ion · 2 copies · chains B

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

Pockets

20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1029	0.90	0.92	125	empty
2	766	0.89	0.93	110	empty
3	726	0.87	0.90	125	empty
4	389	0.82	0.90	65	empty
5	814	0.81	0.84	98	empty

Interfaces

7 interfaces between chains.

D–E · 3051 Å² buried · 43 hydrogen bonds · protein-protein
A–B · 2979 Å² buried · 48 hydrogen bonds · protein-protein
D–F · 1749 Å² buried · 32 hydrogen bonds · protein-protein
A–C · 1747 Å² buried · 32 hydrogen bonds · protein-protein
E–F · 1193 Å² buried · 18 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 7 disulfide (disulfide).

Compared structures

3RFZ · Crystal structure of the FimD usher bound to its cognate FimC:FimH substrate · the same entry in another collection · chain F against F, TM-score 1.00
P59590 · AlphaFold monomer V2.0 prediction for chaperone protein fimc (P59590) · a predicted model of the same protein · chain C against A, TM-score 0.99

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 Q5D223
Every structure of UniProt C6UL88
Every structure of UniProt P59590
Elsewhere: RCSB PDB 3RFZ · PDBe 3RFZ · UniProt Q5D223 · UniProt C6UL88 · UniProt P59590

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