MolNFT v1 · #64493 · protein

Crystal structure of nisod Y9F mutant

3G4X · Superoxide dismutase [ni]: “Crystal structure of nisod Y9F mutant”. X-ray diffraction, 2 ligands (NI, CL), 1 pocket (best druggability 0.38). MolNFT v1 #64493 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 3G4X
Type: protein
Length: 350 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Superoxide dismutase [ni]
EC: 1.15.1.1
UniProt: P80735
Ligands: NI, CL
Pockets: 1 · best druggability 0.38

Structure

x-ray diffraction · 2 distinct chains · 78% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Superoxide dismutase [ni] (EC 1.15.1.1)	protein	117	78% helix, 0% strand	P80735
C	Superoxide dismutase [ni] (EC 1.15.1.1)	protein	116	78% helix, 0% strand	P80735

Ligands and binding sites

NI · Nickel (II) ion · metal · 3 copies · chains A, B, C
CL · Chloride ion · ion · 3 copies · chains A, B, C

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

Pockets

1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	90	0.38	0.76	23	empty

Interfaces

3 interfaces between chains.

A–C · 340 Å² buried · 5 hydrogen bonds · protein-protein
A–B · 330 Å² buried · 6 hydrogen bonds · protein-protein
B–C · 330 Å² buried · 6 hydrogen bonds · protein-protein

Compared structures

3G4X · Crystal Structure of NiSOD Y9F mutant · the same entry in another collection · chain A against A, TM-score 1.00
P80735 · AlphaFold monomer V2.0 prediction for superoxide dismutase [ni] (P80735) · 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 P80735
Elsewhere: RCSB PDB 3G4X · PDBe 3G4X · UniProt P80735

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