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Mouse-human SOD1 chimera

Analyse Mouse-human SOD1 chimera in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3LTV
Type: protein
Length: 914 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Superoxide dismutase [cu-ZN],SUPEROXIDE dismutase [cu-zn]
EC: 1.15.1.1
UniProt: P08228, P00441
Ligands: ZN
Pockets: 7 · best druggability 0.76

Structure

x-ray diffraction · 3 distinct chains · 7% helix, 40% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, E, F	Superoxide dismutase [cu-ZN],SUPEROXIDE dismutase [cu-zn] (EC 1.15.1.1)	protein	153	9% helix, 41% strand	P08228, P00441
C	Superoxide dismutase [cu-ZN],SUPEROXIDE dismutase [cu-zn] (EC 1.15.1.1)	protein	150	5% helix, 40% strand	P08228, P00441
D	Superoxide dismutase [cu-ZN],SUPEROXIDE dismutase [cu-zn] (EC 1.15.1.1)	protein	152	6% helix, 39% strand	P08228, P00441

Ligands and binding sites

ZN · Zinc ion · metal · 6 copies · chains A, B, C, D, E, F

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

Pockets

7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1025	0.76	0.79	90	empty
2	907	0.70	0.75	60	empty
3	230	0.58	0.79	33	empty
4	250	0.58	0.79	32	empty
5	230	0.56	0.79	31	empty

Interfaces

8 interfaces between chains.

E–F · 676 Å² buried · 5 hydrogen bonds · protein-protein
A–B · 674 Å² buried · 4 hydrogen bonds · protein-protein
C–D · 649 Å² buried · 4 hydrogen bonds · protein-protein
A–F · 335 Å² buried · 4 hydrogen bonds · protein-protein
A–C · 324 Å² buried · 2 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 6 disulfide (disulfide).

Compared structures

3LTV · Mouse-human sod1 chimera · the same entry in another collection · chain F against F, TM-score 1.00
P08228 · AlphaFold monomer V2.0 prediction for superoxide dismutase [cu-zn] (P08228) · a predicted model of the same protein · chain D against A, TM-score 0.99

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 P08228
Every structure of UniProt P00441
Elsewhere: RCSB PDB 3LTV · PDBe 3LTV · UniProt P08228 · UniProt P00441

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