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Crystal structure of the ternary complex of the E. COLI type 1 pilus proteins fimc, fimi and the N-terminal domain of fimd

Analyse Crystal structure of the ternary complex of the E. COLI type 1 pilus proteins… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7B0X
Type: protein
Length: 467 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Chaperone protein fimc; Fimbrin-like protein fimi; Outer membrane usher protein fimd
UniProt: P31697, P39264, P30130
Pockets: 4 · best druggability 0.62

Structure

x-ray diffraction · 3 distinct chains · 10% helix, 43% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
C	Chaperone protein fimc	protein	211	5% helix, 52% strand	P31697
I	Fimbrin-like protein fimi	protein	137	5% helix, 41% strand	P39264
D	Outer membrane usher protein fimd	protein	119	24% helix, 30% strand	P30130

Ligands and binding sites

EDO · 1,2-ethanediol · additive · chains D

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

Pockets

4 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	461	0.62	0.76	47	empty
2	63	0.54	0.88	21	empty
3	62	0.37	0.79	21	EDO
4	60	0.37	0.79	12	empty

Interfaces

3 interfaces between chains.

C–I · 1936 Å² buried · 52 hydrogen bonds · protein-protein
C–D · 1044 Å² buried · 6 hydrogen bonds · protein-protein
I–D · 225 Å² buried · 2 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 disulfide (disulfide).

Compared structures

7B0X · Crystal structure of the ternary complex of the E. coli type 1 pilus proteins FimC, FimI… · the same entry in another collection · chain C against C, TM-score 1.00
P31697 · AlphaFold monomer V2.0 prediction for chaperone protein fimc (P31697) · a predicted model of the same protein · chain C against A, TM-score 0.96
P30130 · AlphaFold monomer V2.0 prediction for outer membrane usher protein fimd (P30130) · a predicted model of the same protein · chain D against A, TM-score 0.89
P39264 · AlphaFold monomer V2.0 prediction for fimbrin-like protein fimi (P39264) · a predicted model of the same protein · chain I against A, TM-score 0.86

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 P31697
Every structure of UniProt P39264
Every structure of UniProt P30130
Elsewhere: RCSB PDB 7B0X · PDBe 7B0X · UniProt P31697 · UniProt P39264 · UniProt P30130

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