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Crystal structure of staphylococcus aureus hydrolase amia

Analyse Crystal structure of staphylococcus aureus hydrolase amia in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4KNK
Type: protein
Length: 414 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Bifunctional autolysin
EC: 3.5.1.28, 3.2.1.96
UniProt: Q2FZK7
Ligands: NA, ZN
Pockets: 4 · best druggability 0.56

Structure

x-ray diffraction · 2 distinct chains · 36% helix, 13% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Bifunctional autolysin (EC 3.5.1.28, 3.2.1.96)	protein	206	36% helix, 13% strand	Q2FZK7
B	Bifunctional autolysin (EC 3.5.1.28, 3.2.1.96)	protein	208	35% helix, 13% strand	Q2FZK7

Ligands and binding sites

NA · Sodium ion · metal · 3 copies · chains A, B
ZN · Zinc ion · metal · 2 copies · chains A, B
IMD · Imidazole · additive · 3 copies · chains A, B
PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains A, B
FMT · Formic acid · additive · chains A, B
EDO · 1,2-ethanediol · additive · chains A

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

Pockets

4 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	234	0.56	0.78	38	FMT, NA
2	197	0.48	0.75	33	empty
3	136	0.43	0.76	22	empty
4	128	0.43	0.76	22	ZN

Interfaces

1 interface between chains.

A–B · 788 Å² buried · 10 hydrogen bonds · protein-protein

Compared structures

4KNK · Crystal structure of Staphylococcus aureus hydrolase AmiA · the same entry in another collection · chain A against A, TM-score 1.00
Q2FZK7 · AlphaFold monomer V2.0 prediction for bifunctional autolysin (Q2FZK7) · a predicted model of the same protein · chain A 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 Q2FZK7
Elsewhere: RCSB PDB 4KNK · PDBe 4KNK · UniProt Q2FZK7

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