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X-ray reduced catalase 3 from N.CRASSA in cpd I state (0.263 mgy)

Analyse X-ray reduced catalase 3 from N.CRASSA in cpd I state (0.263 mgy) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6NSY
Type: protein
Length: 2,715 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, O
Pockets: 20 · best druggability 0.86

Structure

x-ray diffraction · 4 distinct chains · 33% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Catalase-3 (EC 1.11.1.6)	protein	681	32% helix, 17% strand	Q9C169
B	Catalase-3 (EC 1.11.1.6)	protein	677	33% helix, 18% strand	Q9C169
C	Catalase-3 (EC 1.11.1.6)	protein	679	32% helix, 18% strand	Q9C169
D	Catalase-3 (EC 1.11.1.6)	protein	678	33% helix, 17% strand	Q9C169

Ligands and binding sites

HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains A, D, B, C
O · Oxygen atom · ion · 2 copies · chains C, D
EDO · 1,2-ethanediol · additive · 9 copies · chains A, B, C, D
ACT · Acetate ion · additive · 8 copies · chains A, B, C, D
PEG · Di(hydroxyethyl)ether · additive · 6 copies · chains A, B, C
EOH · Ethanol · additive · 6 copies · chains A, B, D
PGE · Triethylene glycol · additive · 3 copies · chains A, B, C, D
1PE · Pentaethylene glycol · additive · chains B, C
PG4 · Tetraethylene glycol · additive · chains C

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	275	0.86	0.97	53	HEM, ACT, O
2	275	0.85	0.96	48	HEM, ACT
3	284	0.85	0.96	56	HEM, ACT, O
4	259	0.85	0.96	49	HEM, ACT
5	732	0.83	0.86	113	1PE, PEG

Interfaces

6 interfaces between chains.

A–D · 5890 Å² buried · 90 hydrogen bonds · protein-protein
B–C · 5856 Å² buried · 96 hydrogen bonds · protein-protein
B–D · 5075 Å² buried · 71 hydrogen bonds · protein-protein
A–C · 5007 Å² buried · 69 hydrogen bonds · protein-protein
A–B · 2319 Å² buried · 32 hydrogen bonds · protein-protein

Compared structures

6NSY · X-ray reduced Catalase 3 From N.Crassa in Cpd I state (0.263 MGy) · the same entry in another collection · chain B against B, TM-score 1.00
Q9C169 · AlphaFold monomer V2.0 prediction for catalase-3 (Q9C169) · a predicted model of the same protein · chain A 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 6NSY · PDBe 6NSY · UniProt Q9C169

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