MolNFT v1 · #85659 · protein

Catalase 3 from neurospora crassa

4AJ9 · Catalase-3: “Catalase 3 from neurospora crassa”. X-ray diffraction, 1 ligand (HEM), 20 pockets (best druggability 0.85). MolNFT v1 #85659 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4AJ9
Type: protein
Length: 2,716 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
Pockets: 20 · best druggability 0.85

Structure

x-ray diffraction · 4 distinct chains · 33% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Catalase-3 (EC 1.11.1.6)	protein	677	33% helix, 18% strand	Q9C169
B	Catalase-3 (EC 1.11.1.6)	protein	679	32% helix, 18% strand	Q9C169
C	Catalase-3 (EC 1.11.1.6)	protein	682	33% helix, 18% strand	Q9C169
D	Catalase-3 (EC 1.11.1.6)	protein	678	32% helix, 18% strand	Q9C169

Ligands and binding sites

HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains A, B, C, D
1PE · Pentaethylene glycol · additive · 24 copies · chains A, B, C, D
ACT · Acetate ion · additive · 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, 17 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	252	0.85	0.97	51	HEM, ACT
2	1035	0.84	0.85	112	1PE
3	215	0.84	0.97	35	HEM
4	221	0.84	0.96	37	HEM
5	235	0.83	0.96	35	HEM

Interfaces

6 interfaces between chains.

C–D · 5885 Å² buried · 87 hydrogen bonds · protein-protein
A–B · 5793 Å² buried · 86 hydrogen bonds · protein-protein
B–C · 5049 Å² buried · 68 hydrogen bonds · protein-protein
A–D · 5045 Å² buried · 67 hydrogen bonds · protein-protein
B–D · 2311 Å² buried · 34 hydrogen bonds · protein-protein

Compared structures

4AJ9 · Catalase 3 from Neurospora crassa · 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 4AJ9 · PDBe 4AJ9 · UniProt Q9C169

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