MolNFT v1 · #16383 · protein

Acetobacter turbidans alpha-amino acid ester hydrolase S205A mutant complexed with ampicillin

1NX9: “Acetobacter turbidans alpha-amino acid ester hydrolase S205A mutant complexed with ampicillin”. X-ray diffraction, 1 ligand (AIC), 20 pockets (best druggability 0.79). MolNFT v1 #16383 on GenesisL1: 3D structure, binding sites and…

PDB: 1NX9
Type: protein
Length: 2,468 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Alpha-amino acid ester hydrolase
EC: 3.1.1.43
UniProt: Q8VRK8
Ligands: AIC
Pockets: 20 · best druggability 0.79

Structure

x-ray diffraction · 1 distinct chain · 25% helix, 28% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Alpha-amino acid ester hydrolase (EC 3.1.1.43)	protein	617	25% helix, 28% strand	Q8VRK8

Ligands and binding sites

AIC · (2S,5R,6R)-6-{[(2R)-2-amino-2-phenylethanoyl]amino}-3,3-dimethyl-7-oxo-4-thia-1-azabicyclo[3.2.0]heptane-2-carboxylic acid · ligand · 4 copies · chains A, B, C, D
GOL · Glycerol · additive · 4 copies · chains A, B, C, D

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

Pockets

20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1025	0.79	0.81	101	empty
2	973	0.79	0.81	78	empty
3	1156	0.77	0.79	87	empty
4	1138	0.77	0.79	82	empty
5	469	0.70	0.80	46	AIC, GOL

Interfaces

6 interfaces between chains.

A–C · 2301 Å² buried · 19 hydrogen bonds · protein-protein
B–D · 2268 Å² buried · 20 hydrogen bonds · protein-protein
B–C · 1160 Å² buried · 17 hydrogen bonds · protein-protein
A–D · 1150 Å² buried · 16 hydrogen bonds · protein-protein
C–D · 671 Å² buried · 14 hydrogen bonds · protein-protein

Compared structures

1NX9 · Acetobacter turbidans alpha-amino acid ester hydrolase S205A mutant complexed with… · the same entry in another collection · chain A against A, TM-score 1.00

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 Q8VRK8
Elsewhere: RCSB PDB 1NX9 · PDBe 1NX9 · UniProt Q8VRK8

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