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Crystal structure of human mnsod Y166F mutant

Analyse Crystal structure of human mnsod Y166F mutant in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1PL4
Type: protein
Length: 788 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Superoxide dismutase [mn], mitochondrial
EC: 1.15.1.1
UniProt: P04179
Ligands: MN
Pockets: 9 · best druggability 0.50

Structure

x-ray diffraction · 3 distinct chains · 57% helix, 13% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Superoxide dismutase [mn], mitochondrial (EC 1.15.1.1)	protein	198	57% helix, 13% strand	P04179
B	Superoxide dismutase [mn], mitochondrial (EC 1.15.1.1)	protein	196	58% helix, 13% strand	P04179
C, D	Superoxide dismutase [mn], mitochondrial (EC 1.15.1.1)	protein	197	57% helix, 13% strand	P04179

Ligands and binding sites

MN · Manganese (II) 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

9 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	173	0.50	0.77	22	empty
2	275	0.50	0.74	33	empty
3	161	0.49	0.78	22	empty
4	143	0.48	0.78	19	empty
5	150	0.48	0.78	21	empty

Interfaces

6 interfaces between chains.

A–D · 980 Å² buried · 7 hydrogen bonds · protein-protein
B–C · 964 Å² buried · 7 hydrogen bonds · protein-protein
C–D · 908 Å² buried · 13 hydrogen bonds · protein-protein
A–B · 905 Å² buried · 12 hydrogen bonds · protein-protein
A–C · 321 Å² buried · 6 hydrogen bonds · protein-protein

Compared structures

1PL4 · Crystal Structure of human MnSOD Y166F mutant · the same entry in another collection · chain A against A, TM-score 1.00
P04179 · AlphaFold monomer V2.0 prediction for superoxide dismutase [mn], mitochondrial (P04179) · 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 P04179
Elsewhere: RCSB PDB 1PL4 · PDBe 1PL4 · UniProt P04179

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