Research workbench

Cryo-EM structure of the type 1 pilus rod

Analyse Cryo-EM structure of the type 1 pilus rod in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6C53
Type: protein
Length: 1,716 residues
Chains: 11
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Type-1 fimbrial protein, a chain
UniProt: P04128
Pockets: 20 · best druggability 0.75

Structure

electron microscopy · 1 distinct chain · 3% helix, 41% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F, G, H, I, J, K	Type-1 fimbrial protein, a chain	protein	156	3% helix, 41% strand	P04128

Pockets

20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	894	0.75	0.79	88	empty
2	922	0.72	0.77	131	empty
3	446	0.63	0.77	62	empty
4	344	0.63	0.79	48	empty
5	323	0.62	0.79	44	empty

Interfaces

34 interfaces between chains.

B–D · 1622 Å² buried · 44 hydrogen bonds · protein-protein
G–I · 1621 Å² buried · 44 hydrogen bonds · protein-protein
A–B · 1620 Å² buried · 44 hydrogen bonds · protein-protein
F–H · 1618 Å² buried · 44 hydrogen bonds · protein-protein
H–J · 1617 Å² buried · 44 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 11 disulfide (disulfide).

Compared structures

6C53 · Cryo-EM structure of the Type 1 pilus rod · the same entry in another collection · chain E against E, TM-score 1.00
P04128 · AlphaFold monomer V2.0 prediction for type-1 fimbrial protein, a chain (P04128) · a predicted model of the same protein · chain I against A, TM-score 0.95

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 P04128
Elsewhere: RCSB PDB 6C53 · PDBe 6C53 · UniProt P04128

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