MolNFT v1 · #116419 · protein

Human gelsolin from residues GLU28 to ARG161 with calcium

5DD2: “Human gelsolin from residues GLU28 to ARG161 with calcium”. X-ray diffraction, 1 ligand (CA), 3 pockets (best druggability 0.51). MolNFT v1 #116419 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5DD2
Type: protein
Length: 245 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Gelsolin
UniProt: P06396
Ligands: CA
Pockets: 3 · best druggability 0.51

Structure

x-ray diffraction · 2 distinct chains · 20% helix, 33% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
G	Gelsolin	protein	122	20% helix, 33% strand	P06396
A	Gelsolin	protein	123	20% helix, 34% strand	P06396

Ligands and binding sites

CA · Calcium ion · metal · 4 copies · chains G, A
PG0 · 2-(2-methoxyethoxy)ethanol · additive · chains G

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	141	0.51	0.79	17	empty
2	58	0.41	0.81	17	empty
3	53	0.32	0.77	12	empty

Interfaces

1 interface between chains.

G–A · 682 Å² buried · 5 hydrogen bonds · protein-protein

Compared structures

P06396 · AlphaFold monomer V2.0 prediction for gelsolin (P06396) · a predicted model of the same protein · chain A against A, TM-score 0.94

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 5DD2 · PDBe 5DD2 · UniProt P06396

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