MolNFT v1 · #128851 · protein

Domain swap dimer of the G167R variant of gelsolin second domain

5O2Z: “Domain swap dimer of the G167R variant of gelsolin second domain”. X-ray diffraction, 2 ligands (CA, NA), 1 pocket (best druggability 0.40). MolNFT v1 #128851 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5O2Z
Type: protein
Length: 213 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Gelsolin
UniProt: P06396
Ligands: CA, NA
Pockets: 1 · best druggability 0.40

Structure

x-ray diffraction · 2 distinct chains · 26% helix, 27% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
B	Gelsolin	protein	109	26% helix, 27% strand	P06396
A	Gelsolin	protein	104	27% helix, 28% strand	P06396

Ligands and binding sites

CA · Calcium ion · metal · 2 copies · chains B, A
NA · Sodium ion · metal · 2 copies · chains B, A
FLC · Citrate anion · additive · 2 copies · chains B, A
ACT · Acetate ion · additive · 2 copies · chains B, A
GOL · Glycerol · additive · chains A

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	130	0.40	0.75	32	CA, FLC

Interfaces

1 interface between chains.

B–A · 2114 Å² buried · 51 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 disulfide (disulfide).

Compared structures

5O2Z · Domain swap dimer of the G167R variant of gelsolin second domain · the same entry in another collection · chain B against B, TM-score 1.00
P06396 · AlphaFold monomer V2.0 prediction for gelsolin (P06396) · a predicted model of the same protein · chain A against A, TM-score 0.80

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 P06396
Elsewhere: RCSB PDB 5O2Z · PDBe 5O2Z · UniProt P06396

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