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Crystal structure of native alpha-1-antitrypsin with seven stabilising mutations

Analyse Crystal structure of native alpha-1-antitrypsin with seven stabilising mutations in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5NBU
Type: protein
Length: 370 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Alpha-1-antitrypsin
UniProt: P01009
Ligands: OXM
Pockets: 3 · best druggability 0.51

Structure

x-ray diffraction · 1 distinct chain · 30% helix, 31% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Alpha-1-antitrypsin	protein	370	30% helix, 31% strand	P01009

Ligands and binding sites

OXM · Oxamic acid · ligand · 2 copies · chains A
GOL · Glycerol · additive · 2 copies · chains A

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

Pockets

3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	53	0.51	0.88	16	empty
2	124	0.50	0.80	27	OXM
3	54	0.30	0.76	15	empty

Compared structures

5NBU · Crystal structure of native alpha-1-antitrypsin with seven stabilising mutations · the same entry in another collection · chain A against A, TM-score 1.00
P01009 · AlphaFold monomer V2.0 prediction for alpha-1-antitrypsin (P01009) · 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 P01009
Elsewhere: RCSB PDB 5NBU · PDBe 5NBU · UniProt P01009

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