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Structural basis for the catalytic activity of thermomonospora curvata heme-containing dyp-type peroxidase.

Analyse Structural basis for the catalytic activity of thermomonospora curvata… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5JXU
Type: protein
Length: 720 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Dyp-type peroxidase family
UniProt: D1A807
Ligands: HEM
Pockets: 7 · best druggability 0.84

Structure

x-ray diffraction · 1 distinct chain · 28% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Dyp-type peroxidase family	protein	360	28% helix, 23% strand	D1A807

Ligands and binding sites

HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, B

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

Pockets

7 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	440	0.84	0.92	59	HEM
2	425	0.84	0.91	55	HEM
3	390	0.76	0.86	44	empty
4	258	0.59	0.80	35	empty
5	246	0.59	0.80	35	empty

Interfaces

1 interface between chains.

A–B · 2399 Å² buried · 40 hydrogen bonds · protein-protein

Compared structures

5JXU · Structural basis for the catalytic activity of Thermomonospora curvata heme-containing… · the same entry in another collection · chain A against A, TM-score 1.00

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Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt D1A807
Elsewhere: RCSB PDB 5JXU · PDBe 5JXU · UniProt D1A807

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