MolNFT v1 · #6172 · protein

Structure of tetragonal crystals of human erythrocyte catalase

1F4J: “Structure of tetragonal crystals of human erythrocyte catalase”. X-ray diffraction, 1 ligand (HEM), 20 pockets (best druggability 0.88). MolNFT v1 #6172 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1F4J
Type: protein
Length: 1,918 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Catalase
EC: 1.11.1.6
UniProt: P04040
Ligands: HEM
Pockets: 20 · best druggability 0.88

Structure

x-ray diffraction · 3 distinct chains · 34% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, D	Catalase (EC 1.11.1.6)	protein	479	34% helix, 19% strand	P04040
B	Catalase (EC 1.11.1.6)	protein	479	34% helix, 19% strand	P04040
C	Catalase (EC 1.11.1.6)	protein	481	33% helix, 19% strand	P04040

Ligands and binding sites

HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains A, D, B, 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	705	0.88	0.92	55	empty
2	403	0.87	0.96	51	empty
3	411	0.87	0.95	53	empty
4	993	0.87	0.88	110	HEM
5	289	0.85	0.96	44	HEM

Interfaces

6 interfaces between chains.

A–D · 4308 Å² buried · 60 hydrogen bonds · protein-protein
B–C · 4298 Å² buried · 64 hydrogen bonds · protein-protein
B–D · 4051 Å² buried · 56 hydrogen bonds · protein-protein
A–C · 4039 Å² buried · 57 hydrogen bonds · protein-protein
C–D · 2064 Å² buried · 26 hydrogen bonds · protein-protein

Compared structures

1F4J · Structure of tetragonal crystals of human erythrocyte catalase · the same entry in another collection · chain D against D, TM-score 1.00
P04040 · AlphaFold monomer V2.0 prediction for catalase (P04040) · 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 P04040
Elsewhere: RCSB PDB 1F4J · PDBe 1F4J · UniProt P04040

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