MolNFT v1 · #140561 · protein

Catpo mutant - T188F

5YEM · Catalase: “Catpo mutant - T188F”. X-ray diffraction, 2 ligands (HEM, CA), 20 pockets (best druggability 0.86). MolNFT v1 #140561 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5YEM
Type: protein
Length: 2,712 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Catalase
EC: 1.11.1.6
UniProt: M4GGR5
Ligands: HEM, CA
Pockets: 20 · best druggability 0.86

Structure

x-ray diffraction · 1 distinct chain · 32% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Catalase (EC 1.11.1.6)	protein	678	32% helix, 19% strand	M4GGR5

Ligands and binding sites

HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains A, C, B, D
CA · Calcium ion · metal · 10 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	1124	0.86	0.87	128	CA
2	269	0.85	0.96	49	HEM
3	1157	0.85	0.86	127	CA
4	266	0.85	0.96	47	HEM
5	261	0.85	0.96	47	HEM

Interfaces

6 interfaces between chains.

B–D · 5780 Å² buried · 91 hydrogen bonds · protein-protein
A–C · 5765 Å² buried · 89 hydrogen bonds · protein-protein
A–D · 5088 Å² buried · 72 hydrogen bonds · protein-protein
B–C · 5083 Å² buried · 65 hydrogen bonds · protein-protein
A–B · 2076 Å² buried · 26 hydrogen bonds · protein-protein

Compared structures

5YEM · CATPO mutant - T188F · the same entry in another collection · 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 M4GGR5
Elsewhere: RCSB PDB 5YEM · PDBe 5YEM · UniProt M4GGR5

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