MolNFT v1 · #110633 · protein

Structure of CFA/I pili major subunit cfab trimer

4Y2L · CFA/I fimbrial subunit B: “Structure of CFA/I pili major subunit cfab trimer”. X-ray diffraction, 1 ligand (CA), 7 pockets (best druggability 0.53). MolNFT v1 #110633 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4Y2L
Type: protein
Length: 891 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: CFA/I fimbrial subunit B
UniProt: E3PPC4
Ligands: CA
Pockets: 7 · best druggability 0.53

Structure

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

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	CFA/I fimbrial subunit B	protein	147	3% helix, 53% strand	E3PPC4
B	CFA/I fimbrial subunit B	protein	148	5% helix, 53% strand	E3PPC4
D, E	CFA/I fimbrial subunit B	protein	150	3% helix, 54% strand	E3PPC4
F	CFA/I fimbrial subunit B	protein	149	5% helix, 54% strand	E3PPC4

Ligands and binding sites

CA · Calcium ion · metal · 2 copies · chains B, F, C
IPA · Isopropyl alcohol · additive · 4 copies · chains A, C, D, E

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

Pockets

7 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	336	0.53	0.74	44	IPA
2	87	0.45	0.81	22	empty
3	101	0.44	0.79	23	IPA
4	77	0.33	0.75	17	empty
5	66	0.32	0.76	18	empty

Interfaces

7 interfaces between chains.

A–E · 1597 Å² buried · 30 hydrogen bonds · protein-protein
D–E · 1596 Å² buried · 33 hydrogen bonds · protein-protein
C–F · 1570 Å² buried · 26 hydrogen bonds · protein-protein
B–F · 1510 Å² buried · 24 hydrogen bonds · protein-protein
A–D · 1429 Å² buried · 27 hydrogen bonds · protein-protein

Compared structures

4Y2L · Structure of CFA/I pili major subunit CfaB trimer · the same entry in another collection · chain F against F, TM-score 1.00
E3PPC4 · AlphaFold monomer V2.0 prediction for CFA/I fimbrial subunit B (E3PPC4) · a predicted model of the same protein · chain A against A, TM-score 0.89

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 E3PPC4
Elsewhere: RCSB PDB 4Y2L · PDBe 4Y2L · UniProt E3PPC4

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