MolNFT v1 · #23917 · protein

Crystal structure of porphyromonas gingivalis sod

1UER · Superoxide dismutase: “Crystal structure of porphyromonas gingivalis sod”. X-ray diffraction, 1 ligand (FE), 4 pockets (best druggability 0.74). MolNFT v1 #23917 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1UER
Type: protein
Length: 764 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Superoxide dismutase
EC: 1.15.1.1
UniProt: P19665
Ligands: FE
Pockets: 4 · best druggability 0.74

Structure

x-ray diffraction · 1 distinct chain · 53% helix, 12% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Superoxide dismutase (EC 1.15.1.1)	protein	191	53% helix, 12% strand	P19665

Ligands and binding sites

FE · Fe (III) ion · metal · 4 copies · chains A, B, C, D

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

4 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	393	0.74	0.85	42	empty
2	191	0.55	0.79	25	empty
3	187	0.54	0.79	20	empty
4	202	0.54	0.78	21	empty

Interfaces

4 interfaces between chains.

A–B · 963 Å² buried · 12 hydrogen bonds · protein-protein
C–D · 958 Å² buried · 11 hydrogen bonds · protein-protein
A–D · 311 Å² buried · 6 hydrogen bonds · protein-protein
A–C · 229 Å² buried · 1 hydrogen bond · protein-protein

Compared structures

1UER · Crystal structure of Porphyromonas gingivalis SOD · the same entry in another collection · chain A against A, TM-score 1.00
P19665 · AlphaFold monomer V2.0 prediction for superoxide dismutase [MN/FE] (P19665) · 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 P19665
Elsewhere: RCSB PDB 1UER · PDBe 1UER · UniProt P19665

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