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Crystal structure of an activity-based probe hne complex

Analyse Crystal structure of an activity-based probe hne complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4WVP
Type: protein
Length: 221 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Neutrophil elastase; Btn-3V3-nlb-omt-oic-3V2
EC: 3.4.21.37
UniProt: P08246
Ligands: BTN, 3V3, 3V2, NAG, FUC, BMA, SO4
Pockets: 1 · best druggability 0.52

Structure

x-ray diffraction · 2 distinct chains · 8% helix, 40% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
E	Neutrophil elastase (EC 3.4.21.37)	protein	218	8% helix, 40% strand	P08246
I	Btn-3V3-nlb-omt-oic-3V2	protein	3	0% helix, 33% strand	—

Ligands and binding sites

BTN · Biotin · ligand · chains E, I
3V3 · 1-amino-3,6,9,12-tetraoxapentadecan-15-oic acid · ligand · chains E, I
3V2 · [(1R)-1-aminopropyl]phosphonic acid · ligand · chains E, I
NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains E
FUC · alpha-L-fucopyranose · sugar · 2 copies · chains E
BMA · beta-D-mannopyranose · sugar
SO4 · Sulfate ion · ion · 3 copies · chains E, I
EDO · 1,2-ethanediol · additive · 6 copies · chains E

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

Pockets

1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	98	0.52	0.83	18	empty

Interfaces

1 interface between chains.

E–I · 418 Å² buried · 4 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide, 3 covalent, 3 modified, 2 glycan (disulfide, covalent ligand, N-glycosylation, nonstandard, oxidation).

Compared structures

4WVP · Crystal structure of an activity-based probe HNE complex · the same entry in another collection · chain E against E, TM-score 1.00
P08246 · AlphaFold monomer V2.0 prediction for neutrophil elastase (P08246) · a predicted model of the same protein · chain E against A, TM-score 1.00

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 P08246
Elsewhere: RCSB PDB 4WVP · PDBe 4WVP · UniProt P08246

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