MolNFT v1 · #104042 · protein

1.92 ångström crystal structure of A1AT:TTAI ternary complex

4PYW · Alpha-1-antitrypsin: “1.92 ångström crystal structure of A1AT:TTAI ternary complex”. X-ray diffraction, 2 ligands (ACE, NH2), 4 pockets (best druggability 0.60). MolNFT v1 #104042 on GenesisL1: 3D structure, binding sites and…

PDB: 4PYW
Type: protein
Length: 370 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Alpha-1-antitrypsin; ACE-thr-thr-ala-ile-NH2
UniProt: P01009
Ligands: ACE, NH2
Pockets: 4 · best druggability 0.60

Structure

x-ray diffraction · 2 distinct chains · 30% helix, 32% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Alpha-1-antitrypsin	protein	362	30% helix, 31% strand	P01009
B, C	ACE-thr-thr-ala-ile-NH2	protein	4	0% helix, 50% strand	—

Ligands and binding sites

ACE · Acetyl group · ligand · 2 copies · chains A, B, C
NH2 · Amino group · ion · 2 copies · chains A, B, C
GOL · Glycerol · additive · 2 copies · 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, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	124	0.60	0.85	22	empty
2	88	0.53	0.84	18	GOL
3	72	0.52	0.85	20	empty
4	77	0.33	0.74	17	empty

Interfaces

3 interfaces between chains.

A–C · 474 Å² buried · 12 hydrogen bonds · protein-protein
A–B · 436 Å² buried · 12 hydrogen bonds · protein-protein
B–C · 31 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 covalent (covalent ligand).

Compared structures

4PYW · 1.92 angstrom crystal structure of A1AT:TTAI ternary complex · 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 0.96

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 4PYW · PDBe 4PYW · UniProt P01009

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