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Helicobacter pylori formamidase amif contains a fine-tuned cysteine- glutamate-lysine catalytic triad

Analyse Helicobacter pylori formamidase amif contains a fine-tuned cysteine… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2E2L
Type: protein
Length: 1,901 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Formamidase
EC: 3.5.1.49
UniProt: O25836
Ligands: ARF
Pockets: 5 · best druggability 0.86

Structure

x-ray diffraction · 2 distinct chains · 30% helix, 22% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, F	Formamidase (EC 3.5.1.49)	protein	317	30% helix, 22% strand	O25836
E	Formamidase (EC 3.5.1.49)	protein	316	30% helix, 22% strand	O25836

Ligands and binding sites

ARF · Formamide · ligand · 3 copies · chains A, C, F

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1098	0.86	0.87	127	empty
2	1013	0.86	0.87	121	empty
3	729	0.84	0.87	99	empty
4	108	0.58	0.85	24	empty
5	97	0.56	0.85	20	empty

Interfaces

12 interfaces between chains.

E–F · 4411 Å² buried · 50 hydrogen bonds · protein-protein
A–B · 4402 Å² buried · 50 hydrogen bonds · protein-protein
C–D · 4384 Å² buried · 49 hydrogen bonds · protein-protein
A–D · 531 Å² buried · 6 hydrogen bonds · protein-protein
B–F · 516 Å² buried · 7 hydrogen bonds · protein-protein

Compared structures

2E2L · Helicobacter pylori formamidase AmiF contains a fine-tuned cysteine-glutamate-lysine… · the same entry in another collection · chain F against F, TM-score 1.00
O25836 · AlphaFold monomer V2.0 prediction for formamidase (O25836) · a predicted model of the same protein · chain D 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 O25836
Elsewhere: RCSB PDB 2E2L · PDBe 2E2L · UniProt O25836

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