MolNFT v1 · #62560 · protein

Neurospora crassa catalase-3 crystal structure

3EJ6: “Neurospora crassa catalase-3 crystal structure”. X-ray diffraction, 2 ligands (HEM, NAG), 20 pockets (best druggability 0.85). MolNFT v1 #62560 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 3EJ6
Type: protein
Length: 2,724 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Catalase-3
EC: 1.11.1.6
UniProt: Q9C169
Ligands: HEM, NAG
Pockets: 20 · best druggability 0.85

Structure

x-ray diffraction · 1 distinct chain · 30% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Catalase-3 (EC 1.11.1.6)	protein	681	30% helix, 18% strand	Q9C169

Ligands and binding sites

HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains A, D, B, C
NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains A, B, C, D

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

Pockets

20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	290	0.85	0.96	50	HEM
2	288	0.85	0.96	49	HEM
3	264	0.85	0.96	50	HEM
4	271	0.85	0.96	50	HEM
5	988	0.84	0.85	127	empty

Interfaces

6 interfaces between chains.

A–D · 5889 Å² buried · 94 hydrogen bonds · protein-protein
B–C · 5860 Å² buried · 96 hydrogen bonds · protein-protein
B–D · 5098 Å² buried · 74 hydrogen bonds · protein-protein
A–C · 5077 Å² buried · 76 hydrogen bonds · protein-protein
C–D · 2276 Å² buried · 31 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 glycan (N-glycosylation).

Compared structures

3EJ6 · Neurospora Crassa Catalase-3 Crystal Structure · the same entry in another collection · chain D against D, TM-score 1.00
Q9C169 · AlphaFold monomer V2.0 prediction for catalase-3 (Q9C169) · a predicted model of the same protein · chain C 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 Q9C169
Elsewhere: RCSB PDB 3EJ6 · PDBe 3EJ6 · UniProt Q9C169

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