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Inhibitor bound human angiotensin converting enzyme-related carboxypeptidase (ACE2)

Analyse Inhibitor bound human angiotensin converting enzyme-related carboxypeptidase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1R4L
Type: protein
Length: 655 residues
Chains: 5
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Angiotensin I converting enzyme 2; Disordered segment of collectrin homology domain
UniProt: Q9BYF1
Ligands: XX5, NAG, ZN, CL
Pockets: 4 · best druggability 0.86

Structure

x-ray diffraction · 5 distinct chains · 53% helix, 4% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Angiotensin I converting enzyme 2	protein	597	55% helix, 3% strand	Q9BYF1
B	Disordered segment of collectrin homology domain	protein	6	0% helix, 17% strand	—
C	Disordered segment of collectrin homology domain	protein	20	0% helix, 10% strand	—
D	Disordered segment of collectrin homology domain	protein	18	78% helix, 0% strand	—
E	Disordered segment of collectrin homology domain	protein	14	21% helix, 7% strand	—

Ligands and binding sites

XX5 · (S,S)-2-{1-carboxy-2-[3-(3,5-dichloro-benzyl)-3H-imidazol-4-yl]-ethylamino}-4-methyl-pentanoic acid · ligand · chains A
NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A
ZN · Zinc ion · metal · chains A
CL · Chloride ion · ion · 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, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	808	0.86	0.88	87	ZN, XX5
2	687	0.67	0.76	74	empty
3	64	0.49	0.85	19	empty
4	84	0.46	0.81	21	empty

Interfaces

8 interfaces between chains.

C–E · 254 Å² buried · 3 hydrogen bonds · protein-protein
B–C · 173 Å² buried · 5 hydrogen bonds · protein-protein
D–E · 156 Å² buried · 0 hydrogen bonds · protein-protein
A–C · 138 Å² buried · 1 hydrogen bond · protein-protein
A–E · 78 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 3 disulfide, 2 glycan (disulfide, N-glycosylation).

Compared structures

1R4L · Inhibitor Bound Human Angiotensin Converting Enzyme-Related Carboxypeptidase (ACE2) · the same entry in another collection · chain C against C, TM-score 1.00
3SCI · Crystal structure of spike protein receptor-binding domain from a predicted SARS… · a predicted model of the same protein · chain A against B, TM-score 0.97
3SCK · Crystal structure of spike protein receptor-binding domain from a predicted SARS… · a predicted model of the same protein · chain A against B, TM-score 0.97
3SCJ · Crystal structure of spike protein receptor-binding domain from a predicted SARS… · a predicted model of the same protein · chain A against B, TM-score 0.97
Q9BYF1 · AlphaFold monomer V2.0 prediction for angiotensin-converting enzyme 2 (Q9BYF1) · a predicted model of the same protein · chain A against A, TM-score 0.95
3SCI · Crystal structure of spike protein receptor-binding domain from a predicted SARS… · a predicted model of the same protein · chain A against A, TM-score 0.89
3SCJ · Crystal structure of spike protein receptor-binding domain from a predicted SARS… · a predicted model of the same protein · chain A against A, TM-score 0.88

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 Q9BYF1
Elsewhere: RCSB PDB 1R4L · PDBe 1R4L · UniProt Q9BYF1

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