Research workbench

Structure of I274C variant of E. COLI kate[] - images 31-36

Analyse Structure of I274C variant of E. COLI kate[] - images 31-36 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3PQ7
Type: protein
Length: 2,904 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Catalase hpii
EC: 1.11.1.6
UniProt: P21179
Ligands: HDD, HDE, H2S
Pockets: 20 · best druggability 0.89

Structure

x-ray diffraction · 1 distinct chain · 32% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Catalase hpii (EC 1.11.1.6)	protein	726	32% helix, 18% strand	P21179

Ligands and binding sites

HDD · Cis-heme D hydroxychlorin gamma-spirolactone · ligand · 4 copies · chains A, D, B, C
HDE · Cis-heme D hydroxychlorin gamma-spirolactone 17R, 18S · ligand · 4 copies · chains A, D, B, C
H2S · Hydrosulfuric acid · ion · 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, 18 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	494	0.89	0.96	58	empty
2	488	0.88	0.96	62	empty
3	369	0.86	0.95	44	empty
4	290	0.86	0.96	51	HDD, HDE
5	289	0.85	0.96	49	HDD, HDE

Interfaces

6 interfaces between chains.

A–D · 6217 Å² buried · 118 hydrogen bonds · protein-protein
B–C · 6212 Å² buried · 115 hydrogen bonds · protein-protein
B–D · 5909 Å² buried · 85 hydrogen bonds · protein-protein
A–C · 5875 Å² buried · 83 hydrogen bonds · protein-protein
C–D · 2285 Å² buried · 42 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 covalent (covalent ligand).

Compared structures

3PQ7 · Structure of I274C variant of E. coli KatE[] - Images 31-36 · the same entry in another collection · chain D against D, TM-score 1.00
P21179 · AlphaFold monomer V2.0 prediction for catalase hpii (P21179) · a predicted model of the same protein · chain B 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 P21179
Elsewhere: RCSB PDB 3PQ7 · PDBe 3PQ7 · UniProt P21179

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.