MolNFT v1 · #122401 · protein

Crystal structure of recombinant human Z alpha-1-antitrypsin

5IO1: “Crystal structure of recombinant human Z alpha-1-antitrypsin”. X-ray diffraction, 1 ligand (NAG), 6 pockets (best druggability 0.80). MolNFT v1 #122401 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5IO1
Type: protein
Length: 729 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Alpha-1-antitrypsin
UniProt: P01009
Ligands: NAG
Pockets: 6 · best druggability 0.80

Structure

x-ray diffraction · 2 distinct chains · 29% helix, 31% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Alpha-1-antitrypsin	protein	365	28% helix, 31% strand	P01009
B	Alpha-1-antitrypsin	protein	364	29% helix, 32% strand	P01009

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A, B

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

Pockets

6 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	874	0.80	0.83	83	empty
2	162	0.57	0.82	27	empty
3	60	0.50	0.86	25	empty
4	71	0.50	0.84	24	empty
5	117	0.38	0.74	18	empty

Interfaces

1 interface between chains.

A–B · 950 Å² buried · 15 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 glycan (N-glycosylation).

Compared structures

5IO1 · Crystal structure of recombinant human Z alpha-1-antitrypsin · 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 5IO1 · PDBe 5IO1 · UniProt P01009

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