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Crystal structure of the N-terminal beta-aminopeptidase bapa in complex with pefabloc sc (aebsf)

Analyse Crystal structure of the N-terminal beta-aminopeptidase bapa in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3N33
Type: protein
Length: 1,468 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Beta-peptidyl aminopeptidase
UniProt: Q52VH2
Ligands: AES, SO4
Pockets: 10 · best druggability 0.84

Structure

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

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Beta-peptidyl aminopeptidase	protein	367	28% helix, 28% strand	Q52VH2

Ligands and binding sites

AES · 4-(2-aminoethyl)benzenesulfonyl fluoride · ligand · 8 copies · chains A, B, D, C
SO4 · Sulfate ion · ion · 16 copies · chains A, B, D, C
GOL · Glycerol · additive · 4 copies · chains A, C, B, D
EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · 2 copies · chains A, B, C, D

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

Pockets

10 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1146	0.84	0.85	75	empty
2	638	0.72	0.79	70	EPE, AES, SO4
3	643	0.71	0.79	67	AES, SO4
4	547	0.71	0.80	63	AES, SO4, EPE
5	628	0.70	0.78	65	AES, SO4

Interfaces

6 interfaces between chains.

A–B · 1784 Å² buried · 16 hydrogen bonds · protein-protein
C–D · 1766 Å² buried · 15 hydrogen bonds · protein-protein
B–C · 1446 Å² buried · 24 hydrogen bonds · protein-protein
A–D · 1430 Å² buried · 23 hydrogen bonds · protein-protein
B–D · 941 Å² buried · 15 hydrogen bonds · protein-protein

Compared structures

3N33 · Crystal structure of the N-terminal beta-aminopeptidase BapA in complex with pefabloc SC… · the same entry in another collection · chain D against D, TM-score 1.00
Q52VH2 · AlphaFold monomer V2.0 prediction for beta-peptidyl aminopeptidase bapa (Q52VH2) · a predicted model of the same protein · chain B against A, TM-score 0.98

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 Q52VH2
Elsewhere: RCSB PDB 3N33 · PDBe 3N33 · UniProt Q52VH2

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