Research workbench

Human myeloperoxidase inactivated by TX2

Analyse Human myeloperoxidase inactivated by TX2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3ZS0
Type: protein
Length: 1,140 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Myeloperoxidase light chain; Myeloperoxidase heavy chain
EC: 1.11.2.2
UniProt: P05164
Ligands: ZS0, HEM, NAG, MAN, BMA, FUC, CA, SO4, CL
Pockets: 13 · best druggability 0.80

Structure

x-ray diffraction · 2 distinct chains · 38% helix, 9% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Myeloperoxidase light chain (EC 1.11.2.2)	protein	104	25% helix, 11% strand	P05164
C, D	Myeloperoxidase heavy chain (EC 1.11.2.2)	protein	466	41% helix, 9% strand	P05164

Ligands and binding sites

ZS0 · 3-(4-fluorobenzyl)-2-thioxo-1,2,3,7-tetrahydro-6H-purin-6-one · ligand · 2 copies · chains A, C, B, D
HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, C, B, D
NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains C, D, B, A
MAN · alpha-D-mannopyranose · sugar · 3 copies · chains D, B, A, C
BMA · beta-D-mannopyranose · sugar · 2 copies · chains D, C
FUC · alpha-L-fucopyranose · sugar · 2 copies · chains C, D
CA · Calcium ion · metal · 2 copies · chains A, C, B, D
SO4 · Sulfate ion · ion · 3 copies · chains B, D, A, C
CL · Chloride ion · ion · 2 copies · chains A, C, B, D
ACT · Acetate ion · additive · 6 copies · chains C, D

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

Pockets

13 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	772	0.80	0.83	53	ZS0, HEM
2	705	0.79	0.84	66	MAN, FUC
3	886	0.79	0.81	63	ZS0, HEM
4	82	0.46	0.81	21	empty
5	63	0.45	0.83	20	empty

Interfaces

6 interfaces between chains.

A–C · 5765 Å² buried · 105 hydrogen bonds · protein-protein
B–D · 5683 Å² buried · 101 hydrogen bonds · protein-protein
A–B · 617 Å² buried · 4 hydrogen bonds · protein-protein
C–D · 373 Å² buried · 2 hydrogen bonds · protein-protein
B–C · 255 Å² buried · 2 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 13 disulfide, 6 cofactor, 6 glycan, 2 modified (disulfide, heme attachment, N-glycosylation, oxidation).

Compared structures

3ZS0 · Human Myeloperoxidase inactivated by TX2 · the same entry in another collection · chain A against A, TM-score 1.00
P05164 · AlphaFold monomer V2.0 prediction for myeloperoxidase (P05164) · a predicted model of the same protein · chain C 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 P05164
Elsewhere: RCSB PDB 3ZS0 · PDBe 3ZS0 · UniProt P05164

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