MolNFT v1 · #119954 · protein

Catalase structure determined by electron crystallography of thin 3D crystals

5GKN: “Catalase structure determined by electron crystallography of thin 3D crystals”. Electron crystallography, 2 ligands (HEM, NDP), 20 pockets (best druggability 0.89). MolNFT v1 #119954 on GenesisL1: 3D structure, binding sites and…

PDB: 5GKN
Type: protein
Length: 1,996 residues
Chains: 4
Method: electron crystallography
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Catalase
EC: 1.11.1.6
UniProt: P00432
Ligands: HEM, NDP
Pockets: 20 · best druggability 0.89

Structure

electron crystallography · 1 distinct chain · 33% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Catalase (EC 1.11.1.6)	protein	499	33% helix, 18% strand	P00432

Ligands and binding sites

HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains A, D, B, C
NDP · Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate · ligand · 4 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, 15 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1006	0.89	0.91	152	empty
2	1132	0.89	0.90	166	empty
3	468	0.88	0.95	47	empty
4	467	0.88	0.95	56	empty
5	797	0.86	0.89	51	empty

Interfaces

6 interfaces between chains.

B–C · 4920 Å² buried · 66 hydrogen bonds · protein-protein
A–D · 4904 Å² buried · 61 hydrogen bonds · protein-protein
B–D · 4355 Å² buried · 44 hydrogen bonds · protein-protein
A–C · 4192 Å² buried · 38 hydrogen bonds · protein-protein
C–D · 1944 Å² buried · 15 hydrogen bonds · protein-protein

Compared structures

5GKN · Catalase structure determined by electron crystallography of thin 3D crystals · the same entry in another collection · chain B against B, TM-score 1.00
P00432 · AlphaFold monomer V2.0 prediction for catalase (P00432) · 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 P00432
Elsewhere: RCSB PDB 5GKN · PDBe 5GKN · UniProt P00432

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